Inhibitory effects of extracellular self-DNA: a general biological process?

Viral Recognition and Evasion in Plants

Viruses, causal agents of devastating diseases in plants, are obligate intracellular pathogens composed of a nucleic acid genome and a limited number of viral proteins. The diversity of plant viruses, their diminutive molecular nature, and their symplastic localization pose challenges to understanding the interplay between these pathogens and their hosts in the currently accepted framework of plant innate immunity. It is clear, nevertheless, that plants can recognize the presence of a virus and activate antiviral immune responses, although our knowledge of the breadth of invasion signals and the underpinning sensing events is far from complete. Below, I discuss some of the demonstrated or hypothesized mechanisms enabling viral recognition in plants, the step preceding the onset of antiviral immunity, as well as the strategies viruses have evolved to evade or suppress their detection.

Extracellular Self-DNA Effects on Yeast Cell Cycle and Transcriptome during Batch Growth

The cell cycle and the transcriptome dynamics of yeast exposed to extracellular self-DNA during an aerobic batch culture on glucose have been investigated using cytofluorimetric and RNA-seq analyses. In parallel, the same study was conducted on yeast cells growing in the presence of (heterologous) nonself-DNA. The self-DNA treatment determined a reduction in the growth rate and a major elongation of the diauxic lag phase, as well as a significant delay in the achievement of the stationary phase. This was associated with significant changes in the cell cycle dynamics, with slower exit from the G0 phase, followed by an increased level of cell percentage in the S phase, during the cultivation. Comparatively, the exposure to heterologous DNA did not affect the growth curve and the cell cycle dynamics. The transcriptomic analysis showed that self-DNA exposure produced a generalized downregulation of transmembrane transport and an upregulation of genes associated with sulfur compounds and the pentose phosphate pathway. Instead, in the case of the nonself treatment, a clear response to nutrient deprivation was detected. Overall, the presented findings represent further insights into the complex functional mechanisms of self-DNA inhibition.

Extracellular Self- and Non-Self DNA Involved in Damage Recognition in the Mistletoe Parasitism of Mesquite Trees

Psittacanthus calyculatus parasitizes mesquite trees through a specialized structure called a haustorium, which, in the intrusive process, can cause cellular damage in the host tree and release DAMPs, such as ATP, sugars, RNA, and DNA. These are highly conserved molecules that primarily function as signals that trigger and activate the defense responses. In the present study, we generate extracellular DNA (exDNA) from mesquite (P. laevigata) tree leaves (self-exDNA) and P. calyculatus (non-self exDNA) mistletoe as DAMP sources to examine mesquite trees' capacity to identify specific self or non-self exDNA. We determined that mesquite trees perceive self- and non-self exDNA with the synthesis of O2•-, H2O2, flavonoids, ROS-enzymes system, MAPKs activation, spatial concentrations of JA, SA, ABA, and CKs, and auxins. Our data indicate that self and non-self exDNA application differs in oxidative burst, JA signaling, MAPK gene expression, and scavenger systems. This is the first study to examine the molecular biochemistry effects in a host tree using exDNA sources derived from a mistletoe.

Extracellular DNA secreted in yeast cultures is metabolism-specific and inhibits cell proliferation

Extracellular DNA (exDNA) can be actively released by living cells and different putative functions have been attributed to it. Further, homologous exDNA has been reported to exert species-specific inhibitory effects on several organisms. Here, we demonstrate by different experimental evidence, including 1H-NMR metabolomic fingerprint, that the growth rate decline in Saccharomyces cerevisiae fed-batch cultures is determined by the accumulation of exDNA in the medium. Sequencing of such secreted exDNA represents a portion of the entire genome, showing a great similarity with extrachromosomal circular DNA (eccDNA) already reported inside yeast cells. The recovered DNA molecules were mostly single strands and specifically associated to the yeast metabolism displayed during cell growth. Flow cytometric analysis showed that the observed growth inhibition by exDNA corresponded to an arrest in the S phase of the cell cycle. These unprecedented findings open a new scenario on the functional role of exDNA produced by living cells.

The secreted PAMP-induced peptide StPIP1_1 activates immune responses in potato

Treatment of potato plants with the pathogen-associated molecular pattern Pep-13 leads to the activation of more than 1200 genes. One of these, StPIP1_1, encodes a protein of 76 amino acids with sequence homology to PAMP-induced secreted peptides (PIPs) from Arabidopsis thaliana. Expression of StPIP1_1 is also induced in response to infection with Phytophthora infestans, the causal agent of late blight disease. Apoplastic localization of StPIP1_1-mCherry fusion proteins is dependent on the presence of the predicted signal peptide. A synthetic peptide corresponding to the last 13 amino acids of StPIP1_1 elicits the expression of the StPIP1_1 gene itself, as well as that of pathogenesis related genes. The oxidative burst induced by exogenously applied StPIP1_1 peptide in potato leaf disks is dependent on functional StSERK3A/B, suggesting that StPIP1_1 perception occurs via a receptor complex involving the co-receptor StSERK3A/B. Moreover, StPIP1_1 induces expression of FRK1 in Arabidopsis in an RLK7-dependent manner. Expression of an RLK from potato with high sequence homology to AtRLK7 is induced by StPIP1_1, by Pep-13 and in response to infection with P. infestans. These observations are consistent with the hypothesis that, upon secretion, StPIP1_1 acts as an endogenous peptide required for amplification of the defense response.

Process based modelling of plants-fungus interactions explains fairy ring types and dynamics

Many mushroom-forming fungi can develop circular colonies affecting the vegetation in a phenomenon named fairy rings. Since the nineteenth century, several hypotheses have been proposed to explain how fairy ring fungi form ring-like shapes instead of disks and why they produce negative or positive effects on the surrounding vegetation. In this context, we present a novel process-based mathematical model aimed at reproducing the mycelial spatial configuration of fairy rings and test different literature-supported hypotheses explaining the suppressive and stimulating effects of fungi on plants. Simulations successfully reproduced the shape of fairy rings through the accumulation of fungal self-inhibitory compounds. Moreover, regarding the negative effects of fungi on vegetation, results suggest that fungal-induced soil hydrophobicity is sufficient to reproduce all observed types of fairy rings, while the potential production of phytotoxins is not. In relation to the positive effects of fungi on plants, results show that the release of phytostimulants is needed to reproduce the vegetation patterns associated to some fairy ring types. Model outputs can guide future experiments and field work to corroborate the considered hypotheses and provide more information for further model improvements.

Modelling how negative plant-soil feedbacks across life stages affect the spatial patterning of trees

In this work, we theoretically explore how litter decomposition processes and soil-borne pathogens contribute to negative plant-soil feedbacks, in particular in transient and stable spatial organisation of tropical forest trees and seedlings known as Janzen-Connell distributions. By considering soil-borne pathogens and autotoxicity both separately and in combination in a phenomenological model, we can study how both factors may affect transient dynamics and emerging Janzen-Connell distributions. We also identify parameter regimes associated with different long-term behaviours. Moreover, we compare how the strength of negative plant-soil feedbacks was mediated by tree germination and growth strategies, using a combination of analytical approaches and numerical simulations. Our interdisciplinary investigation, motivated by an ecological question, allows us to construct important links between local feedbacks, spatial self-organisation, and community assembly. Our model analyses contribute to understanding the drivers of biodiversity in tropical ecosystems, by disentangling the abilities of two potential mechanisms to generate Janzen-Connell distributions. Furthermore, our theoretical results may help guiding future field data analyses by identifying spatial signatures in adult tree and seedling distribution data that may reflect the presence of particular plant-soil feedback mechanisms.

Self-DNA Inhibition in Drosophila melanogaster Development: Metabolomic Evidence of the Molecular Determinants

We investigated the effects of dietary delivered self-DNA in the model insect Drosophila melanogaster. Self-DNA administration resulted in low but significant lethality in Drosophila larvae and considerably extended the fly developmental time. This was characterized by the abnormal persistence of the larvae in the L2 and L3 stages, which largely accounted for the average 72 h delay observed in pupariation, as compared to controls. In addition, self-DNA exposure affected adult reproduction by markedly reducing both female fecundity and fertility, further demonstrating its impact on Drosophila developmental processes. The effects on the metabolites of D. melanogaster larvae after exposure to self-DNA were studied by NMR, LC-MS, and molecular networking. The results showed that self-DNA feeding reduces the amounts of all metabolites, particularly amino acids and N-acyl amino acids, which are known to act as lipid signal mediators. An increasing amount of phloroglucinol was found after self-DNA exposure and correlated to developmental delay and egg-laying suppression. Pidolate, a known intermediate in the γ-glutamyl cycle, also increased after exposure to self-DNA and correlated to the block of insect oogenesis.

Shifts of Leaf Litter-Induced Plant-Soil Feedback from Negative to Positive Driven by Ectomycorrhizal Symbiosis between Quercus ilex and Pisolithus arrhizus

Ectomycorrhizas (ECM) are a common symbiotic association between fungi and various plant species in forest ecosystems, affecting community assemblages at the landscape level. ECMs benefit host plants by increasing the surface area for nutrient uptake, defending against pathogens, and decomposing organic matter in the soil. ECM-symbiotic seedlings are also known to perform better in conspecific soils than other species unable to carry the symbiosis, in a process referred to as plant-soil feedback (PSF). In this study, we tested the effects of different leaf litter amendments on ECM and non-ECM seedlings of Quercus ilex inoculated with Pisolithus arrhizus and how they altered the litter-induced PSF. Our experiment showed that the ECM symbiont induced a shift from negative PSF to positive PSF in Q. ilex seedlings by analysing plant and root growth parameters. However, non-ECM seedlings performed better than ECM seedlings in a no-litter condition, indicating an autotoxic effect when litter is present without ECM symbionts. Conversely, ECM seedlings with litter performed better at different decomposition stages, suggesting a possible role of the symbiosis of P. arrhizus and Q. ilex in recycling autotoxic compounds released from conspecific litter, transforming them into nutrients that are transferred to the plant host.

ATM and ATR, two central players of the DNA damage response, are involved in the induction of systemic acquired resistance by extracellular DNA, but not the plant wound response

Background

The plant immune response to DNA is highly self/nonself-specific. Self-DNA triggered stronger responses by early immune signals such as H2O2 formation than nonself-DNA from closely related plant species. Plants lack known DNA receptors. Therefore, we aimed to investigate whether a differential sensing of self-versus nonself DNA fragments as damage- versus pathogen-associated molecular patterns (DAMPs/PAMPs) or an activation of the DNA-damage response (DDR) represents the more promising framework to understand this phenomenon.

Results

We treated Arabidopsis thaliana Col-0 plants with sonicated self-DNA from other individuals of the same ecotype, nonself-DNA from another A. thaliana ecotype, or nonself-DNA from broccoli. We observed a highly self/nonself-DNA-specific induction of H2O2 formation and of jasmonic acid (JA, the hormone controlling the wound response to chewing herbivores) and salicylic acid (SA, the hormone controlling systemic acquired resistance, SAR, to biotrophic pathogens). Mutant lines lacking Ataxia Telangiectasia Mutated (ATM) or ATM AND RAD3-RELATED (ATR) - the two DDR master kinases - retained the differential induction of JA in response to DNA treatments but completely failed to induce H2O2 or SA. Moreover, we observed H2O2 formation in response to in situ-damaged self-DNA from plants that had been treated with bleomycin or SA or infected with virulent bacteria Pseudomonas syringae pv. tomato DC3000 or pv. glycinea carrying effector avrRpt2, but not to DNA from H2O2-treated plants or challenged with non-virulent P. syringae pv. glycinea lacking avrRpt2.

Conclusion

We conclude that both ATM and ATR are required for the complete activation of the plant immune response to extracellular DNA whereas an as-yet unknown mechanism allows for the self/nonself-differential activation of the JA-dependent wound response.

Self-DNA Early Exposure in Cultivated and Weedy Setaria Triggers ROS Degradation Signaling Pathways and Root Growth Inhibition

The accumulation of fragmented extracellular DNA reduces conspecific seed germination and plantlet growth in a concentration-dependent manner. This self-DNA inhibition was repeatedly reported, but the underlying mechanisms are not fully clarified. We investigated the species-specificity of self-DNA inhibition in cultivated vs. weed congeneric species (respectively, Setaria italica and S. pumila) and carried out a targeted real-time qPCR analysis under the hypothesis that self-DNA elicits molecular pathways that are responsive to abiotic stressors. The results of a cross-factorial experiment on root elongation of seedlings exposed to self-DNA, congeneric DNA, and heterospecific DNA from Brassica napus and Salmon salar confirmed a significantly higher inhibition by self-DNA as compared to non-self-treatments, with the latter showing a magnitude of the effect consistent with the phylogenetic distance between the DNA source and the target species. Targeted gene expression analysis highlighted an early activation of genes involved in ROS degradation and management (FSD2, ALDH22A1, CSD3, MPK17), as well as deactivation of scaffolding molecules acting as negative regulators of stress signaling pathways (WD40-155). While being the first exploration of early response to self-DNA inhibition at molecular level on C4 model plants, our study highlights the need for further investigation of the relationships between DNA exposure and stress signaling pathways by discussing potential applications for species-specific weed control in agriculture.

Oligonucleotide Insecticides for Green Agriculture: Regulatory Role of Contact DNA in Plant-Insect Interactions

Insects vastly outnumber us in terms of species and total biomass, and are among the most efficient and voracious consumers of plants on the planet. As a result, to preserve crops, one of the primary tasks in agriculture has always been the need to control and reduce the number of insect pests. The current use of chemical insecticides leads to the accumulation of xenobiotics in ecosystems and a decreased number of species in those ecosystems, including insects. Sustainable development of human society is impossible without useful insects, so the control of insect pests must be effective and selective at the same time. In this article, we show for the first time a natural way to regulate the number of insect pests based on the use of extracellular double-stranded DNA secreted by the plant Pittosporum tobira. Using a principle similar to one found in nature, we show that the topical application of artificially synthesized short antisense oligonucleotide insecticides (olinscides, DNA insecticides) is an effective and selective way to control the insect Coccus hesperidum. Using contact oligonucleotide insecticide Coccus-11 at a concentration of 100 ng/μL on C. hesperidum larvae resulted in a mortality of 95.59 ± 1.63% within 12 days. Green oligonucleotide insecticides, created by nature and later discovered by humans, demonstrate a new method to control insect pests that is beneficial and safe for macromolecular insect pest management.

Metabolomics and molecular networking analyses in Arabidopsis thaliana show that extracellular self-DNA affects nucleoside/nucleotide cycles with accumulation of cAMP, cGMP and N6-methyl-AMP

Extracellular DNA (exDNA) widely occurs in the environment due to release by either cell lysis or active secretion. The role of exDNA in plant-soil interactions has been investigated and inhibitory effects on the growth of conspecific individuals by their self-DNA have been reported. Transcriptome analysis in the model plant Arabidopsis thaliana showed a clear recognition by the plant roots of self- and nonself-exDNA, with inhibition occurring only after exposure to the former. In this study, an untargeted metabolomics approach was used to assess at molecular level the plant reactions to exDNA exposure. Thus, the effects on the metabolites profile of A. thaliana after exposure to self- and nonself-exDNA from plants and fish, were studied by NMR, LC-MS, chemometrics and molecular networking analyses. Results show that self-DNA significantly induces the accumulation of RNA constituents (nucleobases, ribonucleosides, dinucleotide and trinucleotide oligomers). Interestingly, AMP and GMP are found along with their cyclic analogues cAMP and cGMP, and in form of cyclic dimers (c-di-AMP and c-di-GMP). Also methylated adenosine monophosphate (m6AMP) and the dimeric dinucleotide N-methyladenylyl-(3'→5') cytidine (m6ApC) increased only in the self-DNA treatment. Such striking evidence of self-DNA effects highlights a major role of exDNA in plant sensing of its environment.

Field evidence for litter and self-DNA inhibitory effects on Alnus glutinosa roots

Litter decomposition releases nutrients beneficial to plants but also induces phytotoxicity. Phytotoxicity can result from either labile allelopathic compounds or species specific and caused by conspecific DNA. Aquatic plants in flowing water generally do not suffer phytotoxicity because litter is regularly removed. In stagnant water or in litter packs an impact on root functionality can occur. So far, studies on water plant roots have been carried out in laboratory and never in field conditions. The effect of conspecific vs heterospecific litter and purified DNA were assessed on aquatic roots of the riparian woody species Alnus glutinosa L. using a novel method, using closed and open plastic tubes fixed to single roots in the field with closed tubes analogous to stagnant water. Four fresh and four decomposed litter types were used and analysed on extractable C, cellulose, lignin, N content and using ¹³ C-CPMAS NMR spectroscopy. Inhibitory effects were observed with fresh litter in closed systems, with a positive correlation with extractable C and negative with lignin and lignin : N ratio. Alnus self-DNA, but not heterologous one, caused acute toxic effects in the closed system. Our results demonstrate the first field-based evidence for self-DNA inhibition as causal factor of negative feedback between plants and substrate.

Extracellular self-RNA: A danger elicitor in pepper induces immunity against bacterial and viral pathogens in the field

Plants and animals serve as hosts for microbes. To protect themselves from microbe-induced damage, plants and animals need to differentiate self-molecules/signals from non-self, microbe-derived molecules. Damage-associated molecular patterns (DAMPs) are danger signals released from the damaged host tissue or present on the surface of stressed cells. Although a self-extracellular DNA has previously been shown to act as a DAMP in different plant species, the existence of a self-extracellular RNA (eRNA) as a danger signal in plants remains unknown. Here, we firstly evaluated the ability of a pepper self-eRNA to activate immunity against viral and bacterial pathogens under field conditions. Pepper leaves pre-infiltrated with self-eRNA exhibited reduced titer of the naturally occurring Tomato spotted wilt virus and diminished symptoms of Xanthomonas axonopodis pv. vesicatoria infection through eliciting defense priming of abscisic acid signaling. At the end of the growing season at 90 days after transplanting, pepper plants treated with self- and non-self-eRNAs showed no difference in fruit yield. Taken together, our discovery demonstrated that self-eRNA can successfully activate plant systemic immunity without any growth penalty, indicating its potential as a novel disease management agent against a broad range of pathogenic microbes.

NMR Metabolomics and Chemometrics of Lettuce, Lactuca sativa L., under Different Foliar Organic Fertilization Treatments

Lettuce plants were grown in a greenhouse affected by the fungal pathogen Fusarium oxysporum to test the effects on plant metabolomics by different organic treatments. Three foliar application treatments were applied: a commercial compost tea made of aerobically fermented plant organic matter, a pure lyophilized microalga Artrospira platensis, commonly named spirulina, and the same microalga previously exposed during its culture to a natural uptake from medium enriched with F. oxysporum fragmented DNA (NAT). The experiment is the first attempt to observe in field conditions, the use and effects of a natural microbial library as a carrier of pathogenic fungal DNA for disease control. Untargeted NMR metabolomics and chemometrics showed that foliar organic application significantly reduced fumaric and formic acids, aromatic amino acids, and nucleosides, while increasing ethanolamine. A strong decrease in phenolic acids and an increase in citric acid and glutamine were specifically observed in the NAT treatment. It is noteworthy that the exposure of a known biostimulant microalga to fungal DNA in its culture medium was sufficient to induce detectable changes in the metabolomic profiles of the fertilized plants. These findings deserve further investigation to assess the potential relevance of the presented approach in the field of crop biostimulation and biocontrol of plant pathogens.

Effects of Extracellular Self- and Nonself-DNA on the Freshwater Microalga Chlamydomonas reinhardtii and on the Marine Microalga Nannochloropsis gaditana

The role of extracellular DNA (exDNA) in soil and aquatic environments was mainly discussed in terms of source of mineral nutrients and of genetic material for horizontal gene transfer. Recently, the self-exDNA (conspecific) has been shown to have an inhibitory effect on the growth of that organism, while the same was not evident for nonself-exDNA (non conspecific). The inhibitory effect of self-exDNA was proposed as a universal phenomenon, although evidence is mainly reported for terrestrial species. The current study showed the inhibitory effect of self-exDNA also on photosynthetic aquatic microorganisms. We showed that self-exDNA inhibits the growth of the microalgae Chlamydomonas reinhardtii and Nannochloropsis gaditana, a freshwater and a marine species, respectively. In addition, the study also revealed the phenotypic effects post self-exDNA treatments. Indeed, Chlamydomonas showed the formation of peculiar heteromorphic aggregates of palmelloid cells embedded in an extracellular matrix, favored by the presence of DNA in the environment, that is not revealed after exposure to nonself-exDNA. The differential effect of self and nonself-exDNA on both microalgae, accompanied by the inhibitory growth effect of self-exDNA are the first pieces of evidence provided for species from aquatic environments.

Exogenous dsRNA Induces RNA Interference of a Chalcone Synthase Gene in Arabidopsis thaliana

Recent investigations have shown the possibility of artificial induction of RNA interference (RNAi) via plant foliar treatments with naked double-stranded RNA (dsRNA) to silence essential genes in plant fungal pathogens or to target viral RNAs. Furthermore, several studies have documented the downregulation of plant endogenous genes via external application of naked gene-specific dsRNAs and siRNAs to the plant surfaces. However, there are limited studies on the dsRNA processing and gene silencing mechanisms after external dsRNA application. Such studies would assist in the development of innovative tools for crop improvement and plant functional studies. In this study, we used exogenous gene-specific dsRNA to downregulate the gene of chalcone synthase (CHS), the key enzyme in the flavonoid/anthocyanin biosynthesis pathway, in Arabidopsis. The nonspecific NPTII-dsRNA encoding the nonrelated neomycin phosphotransferase II bacterial gene was used to treat plants in order to verify that any observed effects and processing of AtCHS mRNA were sequence specific. Using high-throughput small RNA (sRNA) sequencing, we obtained six sRNA-seq libraries for plants treated with water, AtCHS-dsRNA, or NPTII-dsRNA. After plant foliar treatments, we detected the emergence of a large number of AtCHS- and NPTII-encoding sRNAs, while there were no such sRNAs after control water treatment. Thus, the exogenous AtCHS-dsRNAs were processed into siRNAs and induced RNAi-mediated AtCHS gene silencing. The analysis showed that gene-specific sRNAs mapped to the AtCHS and NPTII genes unevenly with peak read counts at particular positions, involving primarily the sense strand, and documented a gradual decrease in read counts from 17-nt to 30-nt sRNAs. Results of the present study highlight a significant potential of exogenous dsRNAs as a promising strategy to induce RNAi-based downregulation of plant gene targets for plant management and gene functional studies.

The Specificity of Transgene Suppression in Plants by Exogenous dsRNA

The phenomenon of RNA interference (RNAi) is widely used to develop new approaches for crop improvement and plant protection. Recent investigations show that it is possible to downregulate plant transgenes, as more prone sequences to silencing than endogenous genes, by exogenous application of double-stranded RNAs (dsRNAs) and small interfering RNAs (siRNAs). However, there are scarce data on the specificity of exogenous RNAs. In this study, we explored whether plant transgene suppression is sequence-specific to exogenous dsRNAs and whether similar effects can be caused by exogenous DNAs that are known to be perceived by plants and induce certain epigenetic and biochemical changes. We treated transgenic plants of Arabidopsis thaliana bearing the neomycin phosphotransferase II (NPTII) transgene with specific synthetic NPTII-dsRNAs and non-specific dsRNAs, encoding enhanced green fluorescent protein (EGFP), as well as with DNA molecules mimicking the applied RNAs. None of the EGFP-dsRNA doses resulted in a significant decrease in NPTII transgene expression in the NPTII-transgenic plants, while the specific NPTII-dsRNA significantly reduced NPTII expression in a dose-dependent manner. Long DNAs mimicking dsRNAs and short DNA oligonucleotides mimicking siRNAs did not exhibit a significant effect on NPTII transgene expression. Thus, exogenous NPTII-dsRNAs induced a sequence-specific and RNA-specific transgene-suppressing effect, supporting external application of dsRNAs as a promising strategy for plant gene regulation.

Self-DNA Exposure Induces Developmental Defects and Germline DNA Damage Response in Caenorhabditis elegans

Simple Summary

All organisms, from bacteria to mammals, activate responses protecting themselves from dangers represented by outsider invaders and damages. Inappropriately localised self-DNA is one of the molecular clues detected as a danger and triggering defence reactions that may lead to chronic activation of inflammatory conditions. In this study, we investigate if dietary delivered self-DNA is detrimental in a simple metazoan model organism, the nematode Caenorhabditis elegans. Adverse effects were observed in the progenies of worms exposed to self-DNA integrated into their bacterial diet. The presence of self-DNA in the food significantly decreased egg deposition, induced high embryo death, and negatively affected larval development. The findings, on the one side, raise interesting questions on the basic molecular mechanisms involved in response to extracellular self-DNA. On the other side, the observed phenomenon suggests possible applications for the biocontrol of parasitic nematodes by appropriate delivery of their self-DNA in their growing environment.

Abstract

All organisms, from bacteria to mammals, sense and respond to foreign nucleic acids to fight infections in order to survive and preserve genome integrity across generations. The innate immune system is an evolutionarily conserved defence strategy. Complex organisms have developed various cellular processes to respond to and recognise not only infections, i.e., pathogen-associated molecular patterns (PAMPs), but also to sense injury and tissue dysfunctions, i.e., damage-associated molecular patterns (DAMPs). Mis-localized self-DNA can be sensed as DAMP by specific DNA-sensing pathways, and self-DNA chronic exposure can be detrimental to the organisms. Here, we investigate the effects of dietary delivered self-DNA in the nematode Caenorhabditis elegans. The hermaphrodite worms were fed on Escherichia coli genomic libraries: a C. elegans library (self) and a legume (Medicago truncatula) library (non-self). We show that the self-library diet affects embryogenesis, larval development and gametogenesis. DNA damage and activation of p53/CEP-1-dependent apoptosis occur in gonadal germ cells. Studies of self-DNA exposure in this model organism were not pursued up to now. The genetic tractability of C. elegans will help to identify the basic molecular pathways involved in such mechanisms. The specificity of the adverse effects associated with a self-DNA enriched diet suggests applications in biological pest control approaches.

Shoot and root insect herbivory change the plant rhizosphere microbiome and affects cabbage-insect interactions through plant-soil feedback

Plant-soil feedback (PSF) may influence plant-insect interactions. Although plant defense differs between shoot and root tissues, few studies have examined root-feeding insect herbivores in a PSF context. We examined here how plant growth and resistance against root-feeding Delia radicum larvae was influenced by PSF. We conditioned soil with cabbage plants that were infested with herbivores that affect D. radicum through plant-mediated effects: leaf-feeding Plutella xylostella caterpillars and Brevicoryne brassicae aphids, root-feeding D. radicum larvae, and/or added rhizobacterium Pseudomonas simiae WCS417r. We analyzed the rhizosphere microbial community, and in a second set of conspecific plants exposed to conditioned soil, we assessed growth, expression of defense-related genes, and D. radicum performance. The rhizosphere microbiome differed mainly between shoot and root herbivory treatments. Addition of Pseudomonas simiae did not influence rhizosphere microbiome composition. Plant shoot biomass, gene expression, and plant resistance against D. radicum larvae was affected by PSF in a treatment-specific manner. Soil conditioning overall reduced plant shoot biomass, Pseudomonas simiae-amended soil causing the largest growth reduction. In conclusion, shoot and root insect herbivores alter the rhizosphere microbiome differently, with consequences for growth and resistance of plants subsequently exposed to conditioned soil.

Extracellular DNA: Insight of a Signal Molecule in Crop Protection

Simple Summary

Agriculture systems use multiple chemical treatments to prevent pests and diseases, and to fertilize plants and eliminate weeds around the crop. These practices are less accepted by the consumers each day, mostly because of the associated environmental, health, and ecological impact; thus, new sustainable green technologies are being developed to replace the use of chemical products. Among green technologies for agriculture practices, the use of plant elicitors represents an alternative with great potential, and extracellular DNA has shown beneficial effects on important production traits such as defence mechanisms, plant growth and development, and secondary metabolites production that results in yield increment and better-quality food. In this review, we reunite experimental evidence of the natural effect that extracellular DNA has on plants. We also aim to contribute a step closer to the agricultural application of extracellular DNA. Additionally, we suggest that extracellular DNA can have a biostimulant effect on plants, and can be applied as a highly sustainable treatment contributing to the circular economy of primary production.

Abstract

Agricultural systems face several challenges in terms of meeting everyday-growing quantities and qualities of food requirements. However, the ecological and social trade-offs for increasing agricultural production are high, therefore, more sustainable agricultural practices are desired. Researchers are currently working on diverse sustainable techniques based mostly on natural mechanisms that plants have developed along with their evolution. Here, we discuss the potential agricultural application of extracellular DNA (eDNA), its multiple functioning mechanisms in plant metabolism, the importance of hormetic curves establishment, and as a challenge: the technical limitations of the industrial scale for this technology. We highlight the more viable natural mechanisms in which eDNA affects plant metabolism, acting as a damage/microbe-associated molecular pattern (DAMP, MAMP) or as a general plant biostimulant. Finally, we suggest a whole sustainable system, where DNA is extracted from organic sources by a simple methodology to fulfill the molecular characteristics needed to be applied in crop production systems, allowing the reduction in, or perhaps the total removal of, chemical pesticides, fertilizers, and insecticides application.

Arabidopsis thaliana Response to Extracellular DNA: Self Versus Nonself Exposure

The inhibitory effect of extracellular DNA (exDNA) on the growth of conspecific individuals was demonstrated in different kingdoms. In plants, the inhibition has been observed on root growth and seed germination, demonstrating its role in plant-soil negative feedback. Several hypotheses have been proposed to explain the early response to exDNA and the inhibitory effect of conspecific exDNA. We here contribute with a whole-plant transcriptome profiling in the model species Arabidopsis thaliana exposed to extracellular self- (conspecific) and nonself- (heterologous) DNA. The results highlight that cells distinguish self- from nonself-DNA. Moreover, confocal microscopy analyses reveal that nonself-DNA enters root tissues and cells, while self-DNA remains outside. Specifically, exposure to self-DNA limits cell permeability, affecting chloroplast functioning and reactive oxygen species (ROS) production, eventually causing cell cycle arrest, consistently with macroscopic observations of root apex necrosis, increased root hair density and leaf chlorosis. In contrast, nonself-DNA enters the cells triggering the activation of a hypersensitive response and evolving into systemic acquired resistance. Complex and different cascades of events emerge from exposure to extracellular self- or nonself-DNA and are discussed in the context of Damage- and Pathogen-Associated Molecular Patterns (DAMP and PAMP, respectively) responses.

The Molecular Information About Deadwood Bacteriomes Partly Depends on the Targeted Environmental DNA

Microbiome studies mostly rely on total DNA extracts obtained directly from environmental samples. The total DNA consists of both intra- and extracellular DNA, which differ in terms of their ecological interpretation. In the present study, we have investigated for the first time the differences among the three DNA types using microbiome sequencing of Picea abies deadwood logs (Hunter decay classes I, III, and V). While the bacterial compositions of all DNA types were comparable in terms of more abundant organisms and mainly depended on the decay class, we found substantial differences between DNA types with regard to less abundant amplicon sequence variants (ASVs). The analysis of the sequentially extracted intra- and extracellular DNA fraction, respectively, increased the ecological depth of analysis compared to the directly extracted total DNA pool. Both DNA fractions were comparable in proportions and the extracellular DNA appeared to persist in the P. abies deadwood logs, thereby causing its masking effect. Indeed, the extracellular DNA masked the compositional dynamics of intact cells in the total DNA pool. Our results provide evidence that the choice of DNA type for analysis might benefit a study’s answer to its respective ecological question. In the deadwood environment researched here, the differential analysis of the DNA types underlined the relevance of Burkholderiales, Rhizobiales and other taxa for P. abies deadwood decomposition and revealed that the role of Acidobacteriota under this scenario might be underestimated, especially compared to Actinobacteriota.

Green pesticide: Tapping to the promising roles of plant secreted small RNAs and responses towards extracellular DNA

The diverse roles of non-coding RNA and DNA in cross-species communication is yet to be revealed. Once thought to only involve intra-specifically in regulating gene expression, the evidence that these genetic materials can also modulate gene expression between species that belong to different kingdoms is accumulating. Plants send small RNAs to the pathogen or parasite when they are being attacked, targeting essential mRNAs for infection or parasitism of the hosts. However, the same survival mechanism is also deployed by the pathogen or parasite to destabilize plant immune responses. In plants, it is suggested that exposure to extracellular self-DNA impedes growth, while to extracellular non-self-DNA induces the modulation of reactive oxygen species, expression of resistance related genes, epigenetic mechanism, or suppression of disease severity. Exploring the potential of secreted RNA and extracellular DNA as a green pesticide could be a promising alternative if we are to provide food for the future global population without further damaging the environment. Hence, some studies on plant secreted RNA and responses towards extracellular DNA are discussed in this review. The precise mode of action of entry and the following cascade of signaling once the plant cell is exposed to secreted RNA or extracellular DNA could be an interesting topic for future research.

Effect of Fragmented DNA From Plant Pathogens on the Protection Against Wilt and Root Rot of Capsicum annuum L. Plants

Chili pepper (Capsicum annuum L.) production is affected by wilt and root rot, the most devastating disease caused by the pathogen complex of oomycete Phytophthora capsici Leon and the fungi Fusarium oxysporum Schlecht and Rhizoctonia solani Kühn, infecting roots, stems, leaves, and fruits. Fungicides are currently inefficient against this disease and have a high environmental impact. The use of elicitors is a sustainable alternative for inducing resistance to wilting and root rot. DNA fragments of an organism's own origin (conspecific or self-DNA) have shown the ability to inhibit growth and activate defense mechanisms in some plant species. In this investigation, the effect of the fragmented DNA mixture of Phytophthora capsici L., Fusarium oxysporum S., and Rhizoctonia solani K. on the protection against wilt and root rot of Capsicum annuum L. plants was evaluated. Changes in plant performance, phenolics, and flavonoids contents, as well as gene expression involved in the production of defense metabolites after the fragmented and unfragmented DNA mixture in three concentrations (20, 60, and 100 μg mL^-1) in chili peppers, were studied. The results obtained showed a decrease in plant height in 60 and 100 μg mL^-1 concentrations in absence of pathogens. Moreover, the treatment with fragmented DNA 100 μg mL^-1 showed significant increase in the content of phenolic compounds and total flavonoids as well as gene expression associated to plant defense in comparison with control plants. Interestingly, foliar application of DNA fragments of the pathogen complex to a concentration of 100 μg mL^-1 caused a 40% decrease in the mortality of infected plants with the pathogens at 30 days post-inoculation compared with control plants inoculated with the pathogen complex but not sprayed with DNA fragments. These results suggested a perspective for application of fragmented DNA of these pathogens at the agricultural level in crop protection strategies to cope with wilt and root rot in Capsicum.

Self-Inhibitory Activity of Trichoderma Soluble Metabolites and Their Antifungal Effects on Fusarium oxysporum

Self-inhibitory processes are a common feature shared by different organisms. One of the main mechanisms involved in these interactions regarding microorganisms is the release of toxic diffusible substances into the environment. These metabolites can exert both antimicrobial effects against other organisms as well as self-inhibitory ones. The in vitro evaluation of these effects against other organisms has been widely used to identify potential biocontrol agents against phytopathogenic microorganisms. In the present study, we performed membrane assays to compare the self-inhibitory effects of soluble metabolites produced by several Trichoderma isolates and their antifungal activity against a phytopathogenic strain of Fusarium oxysporum. The results demonstrated that Trichoderma spp. present a high self-inhibitory activity in vitro, being affected in both their growth rate and the macroscopic structure of their colonies. These effects were highly similar to those exerted against F. oxysporum in the same conditions, showing no significant differences in most cases. Consequently, membrane assays may not be very informative by themselves to assess putative biocontrol capabilities. Therefore, different methods, or a combination of antifungal and self-inhibitory experiments, could be a better approach to evaluate the potential biocontrol activity of microbial strains in order to pre-select them for further in vivo trials.

Single-stranded oligodeoxynucleotides induce plant defence in Arabidopsis thaliana

BACKGROUND AND AIMS

Single-stranded DNA oligodeoxynucleotides (ssODNs) have been shown to elicit immune responses in mammals. In plants, RNA and genomic DNA can activate immunity, although the exact mechanism through which they are sensed is not clear. The aim of this work was to study the possible effect of ssODNs on plant immunity.

KEY RESULTS

The ssODNs IMT504 and 2006 increased protection against the pathogens Pseudomonas syringae pv. tomato DC3000 and Botrytis cinerea but not against tobacco mosaic virus-Cg when infiltrated in Arabidopsis thaliana. In addition, ssODNs inhibited root growth and promoted stomatal closure in a concentration-dependent manner, with half-maximal effective concentrations between 0.79 and 2.06 µm. Promotion of stomatal closure by ssODNs was reduced by DNase I treatment. It was also diminished by the NADPH oxidase inhibitor diphenyleneiodonium and by coronatine, a bacterial toxin that inhibits NADPH oxidase-dependent reactive oxygen species (ROS) synthesis in guard cells. In addition it was found that ssODN-mediated stomatal closure was impaired in bak1-5, bak1-5/bkk1, mpk3 and npr1-3 mutants. ssODNs also induced early expression of MPK3, WRKY33, PROPEP1 and FRK1 genes involved in plant defence, an effect that was reduced in bak1-5 and bak1-5/bkk1 mutants.

CONCLUSIONS

ssODNs are capable of inducing protection against pathogens through the activation of defence genes and promotion of stomatal closure through a mechanism similar to that of other elicitors of plant immunity, which involves the BAK1 co-receptor, and ROS synthesis.

One ring to rule them all: an ecosystem engineer fungus fosters plant and microbial diversity in a Mediterranean grassland

Species coexistence in grasslands is regulated by several environmental factors and interactions with the soil microbial community. Here, the development of the Basidiomycetes fungus Agaricus arvensis, forming fairy rings, in a species-rich Mediterranean grassland, is described. Effects of the mycelial front on plants, fungi and bacteria were assessed by vegetation survey and next generation sequencing approaches. Our results showed a fungal-dependent shift in the community structure operated by a wave-like spread of fairy rings that decreased plant, fungal and bacterial diversity, indicating a detrimental effect of fairy rings on most species. The fairy rings induced successional processes in plants that enhanced the replacement of a community dominated by perennial plants with short-living and fast-growing plant species. In parallel, fungal and bacterial communities showed evident differences in species composition with several taxa associated within distinct sampling zone across the fairy rings. Notably, bacteria belonging to the Burkholderia genus and fungi of the genus Trichoderma increased in response to the advancing mycelium of A. arvensis. The profound changes in community composition and the overall increase in taxa diversity at ecosystemic scale suggest that fairy ring-forming fungi may act as ecosystem engineer species in Mediterranean grasslands.

The Multiple Facets of Plant-Fungal Interactions Revealed Through Plant and Fungal Secretomics

The plant secretome is usually considered in the frame of proteomics, aiming at characterizing extracellular proteins, their biological roles and the mechanisms accounting for their secretion in the extracellular space. In this review, we aim to highlight recent results pertaining to secretion through the conventional and unconventional protein secretion pathways notably those involving plant exosomes or extracellular vesicles. Furthermore, plants are well known to actively secrete a large array of different molecules from polymers (e.g. extracellular RNA and DNA) to small compounds (e.g. ATP, phytochemicals, secondary metabolites, phytohormones). All of these play pivotal roles in plant-fungi (or oomycetes) interactions, both for beneficial (mycorrhizal fungi) and deleterious outcomes (pathogens) for the plant. For instance, recent work reveals that such secretion of small molecules by roots is of paramount importance to sculpt the rhizospheric microbiota. Our aim in this review is to extend the definition of the plant and fungal secretomes to a broader sense to better understand the functioning of the plant/microorganisms holobiont. Fundamental perspectives will be brought to light along with the novel tools that should support establishing an environment-friendly and sustainable agriculture.

Preliminary evidences of the presence of extracellular DNA single stranded forms in soil

The relevance of extracellular DNA (eDNA) in the soil ecosystem is becoming more and more evident to the scientific community by the progressive discovery of functions accompanying to natural gene transformation. However, despite the increased number of published articles dedicated to eDNA in soil, so far only few are focused on its single stranded form (eDNAss). The present paper is the first to investigate the quantitative relevance of eDNAss in the total soil eDNA pool, discriminating between its linear (eDNAssl) and circular (eDNAssc) forms and the respective weakly (wa) and tightly (ta) adsorbed fractions. The results showed the prevalence of eDNAss and its linear form in both the total soil eDNA pool and its wa and ta fractions. Both of the eDNAss fractions (linear and circular) were characterized by small fragments.

TLR9 in MAFLD and NASH: At the Intersection of Inflammation and Metabolism

Toll-Like Receptor 9 (TLR9) is an ancient receptor integral to the primordial functions of inflammation and metabolism. TLR9 functions to regulate homeostasis in a healthy system under acute stress. The literature supports that overactivation of TLR9 under the chronic stress of obesity is a critical driver of the pathogenesis of NASH and NASH-associated fibrosis. Research has focused on the core contributions of the parenchymal and non-parenchymal cells in the liver, adipose, and gut compartments. TLR9 is activated by endogenous circulating mitochondrial DNA (mtDNA). Chronically elevated circulating levels of mtDNA, caused by the stress of overnutrition, are observed in obesity, metabolic dysfunction-associated fatty liver disease (MAFLD), and NASH. Clinical evidence is supportive of TLR9 overactivation as a driver of disease. The role of TLR9 in metabolism and energy regulation may have an underappreciated contribution in the pathogenesis of NASH. Antagonism of TLR9 in NASH and NASH-associated fibrosis could be an effective therapeutic strategy to target both the inflammatory and metabolic components of such a complex disease.

The Role of DNA in the Extracellular Environment: A Focus on NETs, RETs and Biofilms

The capacity to actively release genetic material into the extracellular environment has been reported for bacteria, archaea, fungi, and in general, for microbial communities, but it is also described in the context of multicellular organisms, animals and plants. This material is often present in matrices that locate outside the cells. Extracellular matrices have important roles in defense response and disease in microbes, animal and plants cells, appearing as barrier against pathogen invasion or for their recognition. Specifically, neutrophils extracellular traps (NETs) in animals and root extracellular traps (RETs) in plants, are recognized to be important players in immunity. A growing amount of evidence revealed that the extracellular DNA, in these contexts, plays an active role in the defense action. Moreover, the protective role of extracellular DNA against antimicrobials and mechanical stress also appears to be confirmed in bacterial biofilms. In parallel, recent efforts highlighted different roles of self (homologous) and non-self (heterologous) extracellular DNA, paving the way to discussions on its role as a "Damage-associated molecular pattern" (DAMP). We here provide an evolutionary overview on extracellular DNA in extracellular matrices like RETs, NETs, and microbial biofilms, discussing on its roles and inferring on possible novel functionalities.

Bioinformatics for Marine Products: An Overview of Resources, Bottlenecks, and Perspectives

The sea represents a major source of biodiversity. It exhibits many different ecosystems in a huge variety of environmental conditions where marine organisms have evolved with extensive diversification of structures and functions, making the marine environment a treasure trove of molecules with potential for biotechnological applications and innovation in many different areas. Rapid progress of the omics sciences has revealed novel opportunities to advance the knowledge of biological systems, paving the way for an unprecedented revolution in the field and expanding marine research from model organisms to an increasing number of marine species. Multi-level approaches based on molecular investigations at genomic, metagenomic, transcriptomic, metatranscriptomic, proteomic, and metabolomic levels are essential to discover marine resources and further explore key molecular processes involved in their production and action. As a consequence, omics approaches, accompanied by the associated bioinformatic resources and computational tools for molecular analyses and modeling, are boosting the rapid advancement of biotechnologies. In this review, we provide an overview of the most relevant bioinformatic resources and major approaches, highlighting perspectives and bottlenecks for an appropriate exploitation of these opportunities for biotechnology applications from marine resources.

Salivary DNase II from Laodelphax striatellus acts as an effector that suppresses plant defence

Extracellular DNA, released by damaged plant cells, acts as a damage-associated molecular pattern (DAMP). We demonstrated previously that the small brown planthopper (Laodelphax striatellus, SBPH) secreted DNase II when feeding on artificial diets. However, the function of DNase II in insect feeding remained elusive. The influences of DNase II on SBPHs and rice plants were investigated by suppressing expression of DNase II or by application of heterogeneously expressed DNase II. We demonstrated that DNase II is mainly expressed in the salivary gland and is responsible for DNA-degrading activity of saliva. Knocking down the expression of DNase II resulted in decreased performance of SBPH reared on rice plants. The dsDNase II-treated SBPH did not influenced jasmonic acid (JA), salicylic acid (SA), ethylene (ET) pathways, but elicited a higher level of H2 O2 and callose accumulation. Application of heterogeneously expressed DNase II in DNase II-deficient saliva slightly reduced the wound-induced defence response. We propose a DNase II-based invading model for SBPH feeding on host plants, and provide a potential target for pest management.

Nucleic Acid Sensing in Mammals and Plants: Facts and Caveats

The accumulation of nucleic acids in aberrant compartments is a signal of danger: fragments of cytosolic or extracellular self-DNA indicate cellular dysfunctions or disruption, whereas cytosolic fragments of nonself-DNA or RNA indicate infections. Therefore, nucleic acids trigger immunity in mammals and plants. In mammals, endosomal Toll-like receptors (TLRs) sense single-stranded (ss) or double-stranded (ds) RNA or CpG-rich DNA, whereas various cytosolic receptors sense dsDNA. Although a self/nonself discrimination could favor targeted immune responses, no sequence-specific sensing of nucleic acids has been reported for mammals. Specific immune responses to extracellular self-DNA versus DNA from related species were recently reported for plants, but the underlying mechanism remains unknown. The subcellular localization of mammalian receptors can favor self/nonself discrimination based on the localization of DNA fragments. However, autoantibodies and diverse damage-associated molecular patterns (DAMPs) shuttle DNA through membranes, and most of the mammalian receptors share downstream signaling elements such as stimulator of interferon genes (STING) and the master transcription regulators, nuclear factor (NF)-κB, and interferon regulatory factor 3 (IRF3). The resulting type I interferon (IFN) response stimulates innate immunity against multiple threats-from infection to physical injury or endogenous DNA damage-all of which lead to the accumulation of eDNA or cytoplasmatic dsDNA. Therefore, no or only low selective pressures might have favored a strict self/nonself discrimination in nucleic acid sensing. We conclude that the discrimination between self- and nonself-DNA is likely to be less strict-and less important-than assumed originally.

Extracellular DAMPs in Plants and Mammals: Immunity, Tissue Damage and Repair

Innate immune receptors, well known mediators of response to non-self-molecules and inflammation, also act as mediators of immunity triggered by 'damage-associated molecular patterns' (DAMPs). Pathogen-associated molecular patterns (PAMPs) cause inflammation in mammals and a rapid immune response in plants, while DAMPs trigger more complex responses, including immunity, tissue maintenance and repair. DAMPs, their receptors and downstream transduction mechanisms are often conserved within a kingdom or, due to convergent evolution, are similar across the kingdoms of life. Herein, we describe the dynamics and functionality of specific extracellular DAMP classes and their receptors in immunity, inflammation and repair of tissue damage in plants and mammals.

Exogenous fragmented DNA acts as a damage-associated molecular pattern (DAMP) inducing changes in CpG DNA methylation and defence-related responses in Lactuca sativa

Damage-associated molecular patterns (DAMPs) have been studied recently to understand plant self-nonself recognition in response to attack by biotic and abiotic stresses. Extracellular DNA has emerged as a possible DAMP. As a DAMP DNA seems to function depending on the phylogenetic scale and has been tested in a few plant species. This study aimed to evaluate the possible role of self DNA (sDNA) as a DAMP by analysing changes in CpG DNA methylation and defence-related responses in lettuce (Lactuca sativa L.) as a model plant. sDNA and nonself DNA (nsDNA) from Capsicum chinense Murray (both species belong to the same clade, Asterids) stimulated aberrant seed germination and root growth in lettuce seedlings. Similar resultswere obtained with nsDNA obtained from Acaciella angustissima (Mill.) Britton & Rose plants (belonging to the clade Rosids I), although at significantly higher concentrations. Moreover, in most cases, this behaviour was correlated with hypomethylation of CpG DNA as well as defence responses measured as altered gene expression associated with oxidative burst and production of secondary metabolites (phenylpropanoids) related to coping with stress conditions. Our results suggested that extracellular and fragmented DNA has a role as a DAMP depending on phylogenetic closeness in plants as lettuce, inducing epigenetic, genetic and biochemical changes within the plant. The importance of our results is that, for the first time, they demonstrate that sDNA acts as a DAMP in plants, changing CpG DNA methylation levels as well as increasing the production of secondary metabolites associated with defence responses to stress.

Organic Amendments, Beneficial Microbes, and Soil Microbiota: Toward a Unified Framework for Disease Suppression

Organic amendments (OAs) and soilborne biocontrol agents or beneficial microbes (BMs) have been extensively studied and applied worldwide in most agriculturally important plant species. However, poor integration of research and technical approaches has limited the development of effective disease management practices based on the combination of these two bio-based strategies. Insights into the importance of the plant-associated microbiome for crop productivity, which can be modified or modulated by introducing OAs and/or BMs, are providing novel opportunities to achieve the goal of long-term disease control. This review discusses novel ways of functionally characterizing OAs and how they may be used to promote the effect of added biocontrol agents and/or beneficial soil microbiota to support natural suppressiveness of plant pathogens.

Extracellular self-DNA as a damage-associated molecular pattern (DAMP) that triggers self-specific immunity induction in plants

Mammals sense self or non-self extracellular or extranuclear DNA fragments (hereinafter collectively termed eDNA) as indicators of injury or infection and respond with immunity. We hypothesised that eDNA acts as a damage-associated molecular pattern (DAMP) also in plants and that it contributes to self versus non-self discrimination. Treating plants and suspension-cultured cells of common bean (Phaseolus vulgaris) with fragmented self eDNA (obtained from other plants of the same species) induced early, immunity-related signalling responses such as H₂O₂ generation and MAPK activation, decreased the infection by a bacterial pathogen (Pseudomonas syringae) and increased an indirect defence to herbivores (extrafloral nectar secretion). By contrast, non-self DNA (obtained from lima bean, Phaseolus lunatus, and Acacia farnesiana) had significantly lower or no detectable effects. Only fragments below a size of 700 bp were active, and treating the eDNA preparation DNAse abolished its inducing effects, whereas treatment with RNAse or proteinase had no detectable effect. These findings indicate that DNA fragments, rather than small RNAs, single nucleotides or proteins, accounted for the observed effects. We suggest that eDNA functions a DAMP in plants and that plants discriminate self from non-self at a species-specific level. The immune systems of plants and mammals share multiple central elements, but further work will be required to understand the mechanisms and the selective benefits of an immunity response that is triggered by eDNA in a species-specific manner.

Extracellular DNA in natural environments: features, relevance and applications

Extracellular DNA (exDNA) is abundant in many habitats, including soil, sediments, oceans and freshwater as well as the intercellular milieu of metazoa. For a long time, its origin has been assumed to be mainly lysed cells. Nowadays, research is collecting evidence that exDNA is often secreted actively and is used to perform a number of tasks, thereby offering an attractive target or tool for biotechnological, medical, environmental and general microbiological applications. The present review gives an overview on the main research areas dealing with exDNA, depicts its inherent origins and functions and deduces the potential of existing and emerging exDNA-based applications. Furthermore, it provides an overview on existing extraction methods and indicates common pitfalls that should be avoided whilst working with exDNA.

DNA Damage and Chromatin Conformation Changes Confer Nonhost Resistance: A Hypothesis Based on Effects of Anti-cancer Agents on Plant Defense Responses

Over the last decades, medical research has utilized DNA altering procedures in cancer treatments with the objective of killing cells or suppressing cell proliferation. Simultaneous research related to enhancing disease resistance in plants reported that alterations in DNA can enhance defense responses. These two opposite perspectives have in common their effects on the center for gene transcription, the nuclear chromatin. A review of selected research from both anticancer- and plant defense-related research provides examples of some specific DNA altering actions: DNA helical distortion, DNA intercalation, DNA base substitution, DNA single cleavage by DNases, DNA alkylation/methylation, and DNA binding/exclusion. The actions of the pertinent agents are compared, and their proposed modes of action are described in this study. Many of the DNA specific agents affecting resistance responses in plants, e.g., the model system using pea endocarp tissue, are indeed anticancer agents. The tumor cell death or growth suppression in cancer cells following high level treatments may be accompanied with chromatin distortions. Likewise, in plants, DNA-specific agents activate enhanced expression of many genes including defense genes, probably due to the chromatin alterations resulting from the agents. Here, we propose a hypothesis that DNA damage and chromatin structural changes are central mechanisms in initiating defense gene transcription during the nonhost resistance response in plants.

Biochars from olive mill waste have contrasting effects on plants, fungi and phytoparasitic nematodes

Olive mill waste (OMW), a byproduct from the extraction of olive oil, causes serious environmental problems for its disposal, and extensive efforts have been made to find cost-effective solutions for its management. Biochars produced from OMW were applied as soil amendment and found in many cases to successfully increase plant productivity and suppress diseases. This work aims to characterize biochars obtained by pyrolysis of OMW at 300 °C to 1000 °C using ¹³C NMR spectroscopy, LC-ESI-Q-TOF-MS and SEM (Scanning Electron Microscopy). Chemical characterization revealed that biochar composition varied according to the increase of pyrolysis temperature (PT). Thermal treated materials showed a progressive reduction of alkyl C fractions coupled to the enrichment in aromatic C products. In addition, numerous compounds present in the organic feedstock (fatty acids, phenolic compounds, triterpene acids) reduced (PT = 300 °C) or completely disappeared (PT ≥ 500 °C) in biochars as compared to untreated OMW. PT also affected surface morphology of biochars by increasing porosity and heterogeneity of pore size. The effects of biochars extracts on the growth of different organisms (two plants, one nematode and four fungal species) were also evaluated. When tested on different living organisms, biochars and OMW showed opposite effects. The root growth of Lepidium sativum and Brassica rapa, as well as the survival of the nematode Meloidogyne incognita, were inhibited by the untreated material or biochar produced at 300 °C, but toxicity decreased at higher PTs. Conversely, growth of Aspergillus, Fusarium, Rhizoctonia and Trichoderma fungi was stimulated by organic feedstock, while being inhibited by thermally treated biochars. Our findings showed a pattern of association between specific biochar chemical traits and its biological effects that, once mechanistically explained and tested in field conditions, may lead to effective applications in agriculture.

Pattern recognition receptors and signaling in plant-microbe interactions

Plants solely rely on innate immunity of each individual cell to deal with a diversity of microbes in the environment. Extracellular recognition of microbe- and host damage-associated molecular patterns leads to the first layer of inducible defenses, termed pattern-triggered immunity (PTI). In plants, pattern recognition receptors (PRRs) described to date are all membrane-associated receptor-like kinases or receptor-like proteins, reflecting the prevalence of apoplastic colonization of plant-infecting microbes. An increasing inventory of elicitor-active patterns and PRRs indicates that a large number of them are limited to a certain range of plant groups/species, pointing to dynamic and convergent evolution of pattern recognition specificities. In addition to common molecular principles of PRR signaling, recent studies have revealed substantial diversification between PRRs in their functions and regulatory mechanisms. This serves to confer robustness and plasticity to the whole PTI system in natural infections, wherein different PRRs are simultaneously engaged and faced with microbial assaults. We review the functional significance and molecular basis of PRR-mediated pathogen recognition and disease resistance, and also an emerging role for PRRs in homeostatic association with beneficial or commensal microbes.

Sensing Danger: Key to Activating Plant Immunity

In both plants and animals, defense against pathogens relies on a complex surveillance system for signs of danger. Danger signals may originate from the infectious agent or from the host itself. Immunogenic plant host factors can be roughly divided into two categories: molecules which are passively released upon cell damage ('classical' damage-associated molecular patterns, DAMPs), and peptides which are processed and/or secreted upon infection to modulate the immune response (phytocytokines). We highlight the ongoing challenge to understand how plants sense various danger signals and integrate this information to produce an appropriate immune response to diverse challenges.