Peat substrate amended with chitin modulates the N-cycle, siderophore and chitinase responses in the lettuce rhizobiome

Chitin-induced disease resistance in plants: A review

Chitin is composed of N-acetylglucosamine units. Chitin a polysaccharide found in the cell walls of fungi and exoskeletons of insects and crustaceans, can elicit a potent defense response in plants. Through the activation of defense genes, stimulation of defensive compound production, and reinforcement of physical barriers, chitin enhances the plant's ability to defend against pathogens. Chitin-based treatments have shown efficacy against various plant diseases caused by fungal, bacterial, viral, and nematode pathogens, and have been integrated into sustainable agricultural practices. Furthermore, chitin treatments have demonstrated additional benefits, such as promoting plant growth and improving tolerance to abiotic stresses. Further research is necessary to optimize treatment parameters, explore chitin derivatives, and conduct long-term field studies. Continued efforts in these areas will contribute to the development of innovative and sustainable strategies for disease management in agriculture, ultimately leading to improved crop productivity and reduced reliance on chemical pesticides.

Dynamics of organic acid exudation and rhizobacteria in maize rhizosphere respond to N-CDs

To sustainably feed the growing global population, it is essential to increase crop yields on limited land while reducing the use of fertilizers and agrochemicals. The rhizosphere regulation shows significant potential to address this challenge. Here, foliar applied doping of nitrogen in carbon dots (N-CDs) entered maize leaves, and were transported to the stems and roots. The internalized N-CDs significantly increased the biomass (26.4-93.8%) and photosynthesis (17.0-20.3 %) of maize seedling during the three-week application of N-CDs, providing the substrate for tricarboxylic acid cycle (TCA) in shoots and roots. Correspondingly, more organic acids involved in TCA cycle, such as citric acid (14.0-fold), succinic acid (4.4-fold) and malic acid (3.4-fold), were synthesized and then secreted into rhizosphere after exposed to N-CDs for one day. As the exposure time increased, greater secretion of above organic acids by the roots was induced. However, no significant change was observed in the relative abundance of rhizobacteria after foliar application with N-CDs for one day. After one week, the relative abundances of Azotobacter, Bacillus, Lysobacter, Mucilaginibacter, and Sphingomonas increased by 0.8-3.8 folds. The relative abundance of more beneficial rhizobacteria (Sphingomonas, Lysobacter, Rhizobium, Azotobacter, Pseudomonas, Mucilaginibacter and Bacillus) enriched by 0.3-6.0 folds after two weeks, and Sphingomonas, Flavisolibacter and Bacillus improved by 0.6-3.2 folds after three weeks. These dynamic changes suggested that N-CDs initiate the synthesis and secretion of organic acids and then recruited beneficial rhizobacteria. The hierarchical partitioning analysis further indicated that N-CDs-induced secretion of organic acids from the roots was the main drivers of rhizobacteria community dynamics. The differential microbes altered by N-CDs were mainly involved in nitrogen (N) and phosphorus (P) cycles, which are beneficial for N and P uptake, and maize growth. These results provide insights into understanding the rhizosphere regulation of nanomaterials to improve plant productivity and nutrient-use efficiency.

Microbial Exudates as Biostimulants: Role in Plant Growth Promotion and Stress Mitigation

Microbes hold immense potential, based on the fact that they are widely acknowledged for their role in mitigating the detrimental impacts of chemical fertilizers and pesticides, which were extensively employed during the Green Revolution era. The consequence of this extensive use has been the degradation of agricultural land, soil health and fertility deterioration, and a decline in crop quality. Despite the existence of environmentally friendly and sustainable alternatives, microbial bioinoculants encounter numerous challenges in real-world agricultural settings. These challenges include harsh environmental conditions like unfavorable soil pH, temperature extremes, and nutrient imbalances, as well as stiff competition with native microbial species and host plant specificity. Moreover, obstacles spanning from large-scale production to commercialization persist. Therefore, substantial efforts are underway to identify superior solutions that can foster a sustainable and eco-conscious agricultural system. In this context, attention has shifted towards the utilization of cell-free microbial exudates as opposed to traditional microbial inoculants. Microbial exudates refer to the diverse array of cellular metabolites secreted by microbial cells. These metabolites enclose a wide range of chemical compounds, including sugars, organic acids, amino acids, peptides, siderophores, volatiles, and more. The composition and function of these compounds in exudates can vary considerably, depending on the specific microbial strains and prevailing environmental conditions. Remarkably, they possess the capability to modulate and influence various plant physiological processes, thereby inducing tolerance to both biotic and abiotic stresses. Furthermore, these exudates facilitate plant growth and aid in the remediation of environmental pollutants such as chemicals and heavy metals in agroecosystems. Much like live microbes, when applied, these exudates actively participate in the phyllosphere and rhizosphere, engaging in continuous interactions with plants and plant-associated microbes. Consequently, they play a pivotal role in reshaping the microbiome. The biostimulant properties exhibited by these exudates position them as promising biological components for fostering cleaner and more sustainable agricultural systems.

Abundance, classification and genetic potential of Thaumarchaeota in metagenomes of European agricultural soils: a meta-analysis

BACKGROUND

For a sustainable production of food, research on agricultural soil microbial communities is inevitable. Due to its immense complexity, soil is still some kind of black box. Soil study designs for identifying microbiome members of relevance have various scopes and focus on particular environmental factors. To identify common features of soil microbiomes, data from multiple studies should be compiled and processed. Taxonomic compositions and functional capabilities of microbial communities associated with soils and plants have been identified and characterized in the past few decades. From a fertile Loess-Chernozem-type soil located in Germany, metagenomically assembled genomes (MAGs) classified as members of the phylum Thaumarchaeota/Thermoproteota were obtained. These possibly represent keystone agricultural soil community members encoding functions of relevance for soil fertility and plant health. Their importance for the analyzed microbiomes is corroborated by the fact that they were predicted to contribute to the cycling of nitrogen, feature the genetic potential to fix carbon dioxide and possess genes with predicted functions in plant-growth-promotion (PGP). To expand the knowledge on soil community members belonging to the phylum Thaumarchaeota, we conducted a meta-analysis integrating primary studies on European agricultural soil microbiomes.

RESULTS

Taxonomic classification of the selected soil metagenomes revealed the shared agricultural soil core microbiome of European soils from 19 locations. Metadata reporting was heterogeneous between the different studies. According to the available metadata, we separated the data into 68 treatments. The phylum Thaumarchaeota is part of the core microbiome and represents a major constituent of the archaeal subcommunities in all European agricultural soils. At a higher taxonomic resolution, 2074 genera constituted the core microbiome. We observed that viral genera strongly contribute to variation in taxonomic profiles. By binning of metagenomically assembled contigs, Thaumarchaeota MAGs could be recovered from several European soil metagenomes. Notably, many of them were classified as members of the family Nitrososphaeraceae, highlighting the importance of this family for agricultural soils. The specific Loess-Chernozem Thaumarchaeota MAGs were most abundant in their original soil, but also seem to be of importance in other agricultural soil microbial communities. Metabolic reconstruction of Switzerland_1_MAG_2 revealed its genetic potential i.a. regarding carbon dioxide (CO[Formula: see text]) fixation, ammonia oxidation, exopolysaccharide production and a beneficial effect on plant growth. Similar genetic features were also present in other reconstructed MAGs. Three Nitrososphaeraceae MAGs are all most likely members of a so far unknown genus.

CONCLUSIONS

On a broad view, European agricultural soil microbiomes are similarly structured. Differences in community structure were observable, although analysis was complicated by heterogeneity in metadata recording. Our study highlights the need for standardized metadata reporting and the benefits of networking open data. Future soil sequencing studies should also consider high sequencing depths in order to enable reconstruction of genome bins. Intriguingly, the family Nitrososphaeraceae commonly seems to be of importance in agricultural microbiomes.

Insect exuviae as soil amendment affect flower reflectance and increase flower production and plant volatile emission

Soil composition and herbivory are two environmental factors that can affect plant traits including flower traits, thus potentially affecting plant-pollinator interactions. Importantly, soil composition and herbivory may interact in these effects, with consequences for plant fitness. We assessed the main effects of aboveground insect herbivory and soil amendment with exuviae of three different insect species on visual and olfactory traits of Brassica nigra plants, including interactive effects. We combined various methodological approaches including gas chromatography/mass spectrometry, spectroscopy and machine learning to evaluate changes in flower morphology, colour and the emission of volatile organic compounds (VOCs). Soil amended with insect exuviae increased the total number of flowers per plant and VOC emission, whereas herbivory reduced petal area and VOC emission. Soil amendment and herbivory interacted in their effect on the floral reflectance spectrum of the base part of petals and the emission of 10 VOCs. These findings demonstrate the effects of insect exuviae as soil amendment on plant traits involved in reproduction, with a potential for enhanced reproductive success by increasing the strength of signals attracting pollinators and by mitigating the negative effects of herbivory.

Chitinophaga horti sp. nov., Isolated from Garden Soil

A strictly aerobic Gram-negative bacterium, designated R8^T, isolated from garden soil in South Korea was subjected to a taxonomic study. The cells were non-spore-forming, oxidase-positive and catalase-negative, and non-motile rods (without flagella). Growth was observed between 10 °C and 40 °C (optimum, 30 °C) and between pH 6.0 and 9.0 (optimum, pH 7.0) and in the presence of 0%-1.5% (w/v) NaCl (optimum, 0%). The G + C content of the genomic DNA was 49.9% and the major isoprenoid quinone was found to be menaquinone-7. The major fatty acids of strain R8^T were iso-C_15:0, C_16:1 ω5c, and summed feature 3 (comprising iso-C_15:0 2-OH and/or C_16:1 ω7c/ω6c). Phosphatidylethanolamine was identified as a major polar lipid. Comparative 16S rRNA gene sequence analysis showed that strain R8^T had the highest 16S rRNA gene sequence similarity of 98.3% with Chitinophaga sedimenti TFL-3 ^T. Phylogenetic analyses using 16S rRNA gene sequences and concatenated 92 marker protein sequences revealed that strain R8^T formed a robust phylogenetic lineage with C. sedimenti within the genus Chitinophaga. Average nucleotide identity and digital DNA-DNA hybridization values of strain R8^T to Chitinophaga species were less than 77.9% and 21.1%, respectively. The phenotypic, phylogenetic, and chemotaxonomic properties support that strain R8^T represents a novel species of the genus Chitinophaga, for which the name Chitinophaga horti sp. nov. is proposed. The type strain is R8^T (= KACC 19895 ^T = JCM 33215 ^T).

Assessment of transcriptional reprogramming of lettuce roots in response to chitin soil amendment

Chitin soil amendment is known to improve soil quality, plant growth and stress resilience, but the underlying mechanisms are not well understood. In this study, we monitored chitin's effect on lettuce physiology every two weeks through an eight-week growth period, analyzed the early transcriptional reprogramming and related metabolomic changes of lettuce, in response to crab chitin treatment in peat-based potting soil. In commercial growth conditions, chitin amendment still promoted lettuce growth, increased chlorophyll content, the number of leaves and crop head weight from week six. The flavonoid content in lettuce leaves was altered as well, showing an increase at week two but a decrease from week six. Transcriptomic analysis showed that over 300 genes in lettuce root were significantly differentially expressed after chitin soil treatment. Gene Ontology-term (GO) enrichment analysis revealed statistical overrepresentation of GO terms linked to photosynthesis, pigment metabolic process and phenylpropanoid metabolic process. Further analysis of the differentially expressed genes (DEGs) showed that the flavonoid pathway was mostly upregulated whereas the bifurcation of upstream phenylpropanoid pathway towards lignin biosynthesis was mostly downregulated. Metabolomic analysis revealed the upregulation of salicylic acid, chlorogenic acid, ferulic acid, and p-coumaric acid in chitin-treated lettuce seedlings. These phenolic compounds (PCs) mainly influence the phenylpropanoid biosynthesis pathway and may play important roles in plant defense reactions. Our results suggest that chitin soil amendments might activate induced resistance by priming lettuce plants and promote lettuce growth via transcriptional changes.

Chitin amendments eliminate the negative impacts of continuous cropping obstacles on soil properties and microbial assemblage

Continuous cropping of soybean leads to soil environment deterioration and soil-borne disease exacerbation, which in turn limits the sustainability of agricultural production. Chitin amendments are considered promising methods for alleviating soybean continuous cropping obstacles; however, the underlying mechanisms of soil sickness reduction remain unclear. In this study, soil amendments with pure and crude chitin at different addition dosages were employed to treat diseased soil induced by continuous cropping of soybean for five years. Chitin amendments, especially crude chitin, remarkably increased soil pH, available phosphorus (AP), potassium (AK) and nitrate nitrogen ( NO 3 - -N) contents, and improved soybean plant growth and soil microbial activities (FDA). Additionally, chitin application significantly enriched the relative abundances of the potential biocontrol bacteria Sphingomonas, Streptomyces, and Bacillus and the fungi Mortierella, Purpureocillium, and Metarhizium while depleted those of the potential plant pathogens Fusarium, Cylindrocarpon and Paraphoma. Moreover, chitin amendments induced looser pathogenic subnetwork structures and less pathogenic cooperation with other connected microbial taxa in the rhizosphere soils. The structural equation model (SEM) revealed that pure and crude chitin amendments promoted soybean plant growth by indirectly regulating soil pH-mediated soil microbial activities and potentially beneficial microbes, respectively. Therefore, the reduction strategies for continuous cropping obstacles by adding pure and crude chitin were distinct; pure chitin amendments showed general disease suppression, while crude chitin exhibited specific disease suppression. Overall, chitin amendments could suppress potential plant pathogens and improve soil health, thereby promoting soybean growth, which provides new prospects for cultivation practices to control soybean continuous cropping obstacles.

Insect frass and exuviae to promote plant growth and health

Beneficial soil microorganisms can contribute to biocontrol of plant pests and diseases, induce systemic resistance (ISR) against attackers, and enhance crop yield. Using organic soil amendments has been suggested to stimulate the abundance and/or activity of beneficial indigenous microbes in the soil. Residual streams from insect farming (frass and exuviae) contain chitin and other compounds that may stimulate beneficial soil microbes that have ISR and biocontrol activity. Additionally, changes in plant phenotype that are induced by beneficial microorganisms may directly influence plant-pollinator interactions, thus affecting plant reproduction. We explore the potential of insect residual streams derived from the production of insects as food and feed to promote plant growth and health, as well as their potential benefits for sustainable agriculture.

N-Acetylglucosamine Promotes Tomato Plant Growth by Shaping the Community Structure and Metabolism of the Rhizosphere Microbiome

Communication between plants and microorganisms is vital because it influences their growth, development, defense, propagation, and metabolism in achieving maximal fitness. N-acetylglucosamine (N-GlcNAc), the building block of bacterial and fungal cell walls, was first reported to promote tomato plant growth via stimulation of microorganisms typically known to dominate the tomato root rhizosphere, such as members of Proteobacteria and Actinobacteria. Using KEGG pathway analysis of the rhizosphere microbial operational taxonomic units, the streptomycin biosynthesis pathway was enriched in the presence of N-GlcNAc. The biosynthesis of 3-hydroxy-2-butanone (acetoin) and 2,3-butanediol, two foremost types of plant growth promotion-related volatile organic compounds, were activated in both Bacillus subtilis and Streptomyces thermocarboxydus strains when they were cocultured with N-GlcNAc. In addition, the application of N-GlcNAc increased indole-3-acetic acid production in a dose-dependent manner in strains of Bacillus cereus, Proteus mirabilis, Pseudomonas putida, and S. thermocarboxydus that were isolated from an N-GlcNAc-treated tomato rhizosphere. Overall, this study found that N-GlcNAc could function as microbial signaling molecules to shape the community structure and metabolism of the rhizosphere microbiome, thereby regulating plant growth and development and preventing plant disease through complementary plant-microbe interactions. IMPORTANCE While the benefits of using plant growth-promoting rhizobacteria (PGPRs) to enhance crop production have been recognized and studied extensively under laboratory conditions, the success of their application in the field varies immensely. More fundamentally explicit processes of positive, plant-PGPRs interactions are needed. The utilization of organic amendments, such as chitin and its derivatives, is one of the most economical and practical options for improving soil and substrate quality as well as plant growth and resilience. In this study, we observed that the chitin monomer N-GlcNAc, a key microbial signaling molecule produced through interactions between chitin, soil microbes, and the plants, positively shaped the community structure and metabolism of the rhizosphere microbiome of tomatoes. Our findings also provide a new direction for enhancing the benefits and stability of PGPRs in the field.

UMGAP: the Unipept MetaGenomics Analysis Pipeline

Background

Shotgun metagenomics yields ever richer and larger data volumes on the complex communities living in diverse environments. Extracting deep insights from the raw reads heavily depends on the availability of fast, accurate and user-friendly biodiversity analysis tools.

Results

Because environmental samples may contain strains and species that are not covered in reference databases and because protein sequences are more conserved than the genes encoding them, we explore the alternative route of taxonomic profiling based on protein coding regions translated from the shotgun metagenomics reads, instead of directly processing the DNA reads. We therefore developed the Unipept MetaGenomics Analysis Pipeline (UMGAP), a highly versatile suite of open source tools that are implemented in Rust and support parallelization to achieve optimal performance. Six preconfigured pipelines with different performance trade-offs were carefully selected, and benchmarked against a selection of state-of-the-art shotgun metagenomics taxonomic profiling tools.

Conclusions

UMGAP’s protein space detour for taxonomic profiling makes it competitive with state-of-the-art shotgun metagenomics tools. Despite our design choices of an extra protein translation step, a broad spectrum index that can identify both archaea, bacteria, eukaryotes and viruses, and a highly configurable non-monolithic design, UMGAP achieves low runtime, manageable memory footprint and high accuracy. Its interactive visualizations allow for easy exploration and comparison of complex communities.

Supplementary Information

The online version contains supplementary material available at (10.1186/s12864-022-08542-4).

Tomatoes: An Extensive Review of the Associated Health Impacts of Tomatoes and Factors That Can Affect Their Cultivation

Simple Summary

The research outlined in this review paper discusses potential health benefits associated with a diet enriched with tomatoes and tomato products. This includes details of previous studies investigating the anticancer properties of tomatoes, protection against cardiovascular and neurodegenerative diseases and diabetes, maintenance of a healthy gut microbiome, and improved skin health, fertility, immune response, and exercise recovery. The specific parts of a tomato fruit that contribute these health benefits are also outlined. The potential disadvantages to a tomato-rich diet are detailed, especially the consumption of supplements that contain compounds found in tomatoes, such as lycopene. This review also discusses how the cultivation of tomato plants can affect the nutritional value of the fruit harvested. Different environmental growing conditions such as light intensity, growing media, and temperature are explained in terms of the impact they have on the quality of fruit, its nutrient content, and hence the potential health benefits acquired from eating the fruit.

Abstract

This review outlines the health benefits associated with the regular consumption of tomatoes and tomato products. The first section provides a detailed account of the horticultural techniques that can impact the quality of the fruit and its nutritional properties, including water availability, light intensity, temperature, and growing media. The next section provides information on the components of tomato that are likely to contribute to its health effects. The review then details some of the health benefits associated with tomato consumption, including anticancer properties, cardiovascular and neurodegenerative diseases and skin health. This review also discusses the impact tomatoes can have on the gut microbiome and associated health benefits, including reducing the risk of inflammatory bowel diseases. Other health benefits of eating tomatoes are also discussed in relation to effects on diabetes, the immune response, exercise recovery, and fertility. Finally, this review also addresses the negative effects that can occur as a result of overconsumption of tomato products and lycopene supplements.

Biochar-Enhanced Resistance to Botrytis cinerea in Strawberry Fruits (But Not Leaves) Is Associated With Changes in the Rhizosphere Microbiome

Biochar has been reported to play a positive role in disease suppression against airborne pathogens in plants. The mechanisms behind this positive trait are not well-understood. In this study, we hypothesized that the attraction of plant growth-promoting rhizobacteria (PGPR) or fungi (PGPF) underlies the mechanism of biochar in plant protection. The attraction of PGPR and PGPF may either activate the innate immune system of plants or help the plants with nutrient uptake. We studied the effect of biochar in peat substrate (PS) on the susceptibility of strawberry, both on leaves and fruits, against the airborne fungal pathogen Botrytis cinerea. Biochar had a positive impact on the resistance of strawberry fruits but not the plant leaves. On leaves, the infection was more severe compared with plants without biochar in the PS. The different effects on fruits and plant leaves may indicate a trade-off between plant parts. Future studies should focus on monitoring gene expression and metabolites of strawberry fruits to investigate this potential trade-off effect. A change in the microbial community in the rhizosphere was also observed, with increased fungal diversity and higher abundances of amplicon sequence variants classified into Granulicella, Mucilaginibacter, and Byssochlamys surrounding the plant root, where the latter two were reported as biocontrol agents. The change in the microbial community was not correlated with a change in nutrient uptake by the plant in either the leaves or the fruits. A decrease in the defense gene expression in the leaves was observed. In conclusion, the decreased infection of B. cinerea in strawberry fruits mediated by the addition of biochar in the PS is most likely regulated by the changes in the microbial community.

Microbial chitinases: properties, enhancement and potential applications

Chitinases are a category of hydrolytic enzymes that catalyze chitin and are formed by a wide variety of microorganisms. In nature, microbial chitinases are primarily responsible for chitin decomposition and play a vital role in the balance of carbon and nitrogen ratio in the ecosystem. The physicochemical attributes and the source of chitinase are the main bases that determine their functional characteristics and hydrolyzed products. Several chitinases have been reported and characterized, and they obtain a wider consideration for their utilization in a large number of uses such as in agriculture, food, environment, medicine and pharmaceutical companies. The antifungal and insecticidal impacts of several chitinases have been extensively studied, aiming to protect crops from phytopathogenic fungi and insects. Chitooligosaccharides synthesized by chitin degradation have been shown to improve human health through their antimicrobial, antioxidant, anti-inflammatory and antitumor properties. This review aims at investigating chitinase production, properties and their potential applications in various biotechnological fields.

Chemically versus thermally processed brown shrimp shells or Chinese mitten crab as a source of chitin, nutrients or salts and as microbial stimulant in soilless strawberry cultivation

Brown shrimp (Crangon crangon) shells and Chinese mitten crab (Eriocheir sinensis) were chemically demineralized and deproteinized (denoted as M1 to M4 for the shrimp shells and M5 to M7 for the Chinese mitten crab), and shrimp shells were torrefied at 200 to 300 °C (denoted as R200, R255, R300), and were compared with a commercially available chitin source (denoted as reference chitin). Based on their chemical characteristics, a selection of chitin sources was tested for their N mineralization capacity. The N release was high for the chemically treated shrimp shells and Chinese mitten crab, but not for the torrefied shrimp shells with or without acid treatment, indicating that treatment at 200 °C or higher resulted in low N availability. Interaction with nutrients was tested in a leaching experiment with limed peat for three thermally and two chemically processed shrimp shells and the reference chitin source. The K concentrations in the leachate for the chemically treated shrimp shells and the reference chitin were lower than for limed peat during fertigation. Irreversible K retention was observed for one source of chemically treated shrimp shells, and the reference chitin. The thermally treated shrimp shells had a significantly higher net release of P, Na and Cl than the treatment without chitin source. Three shrimp shell based materials (M4, R200 and R300) and the reference chitin were tested in a greenhouse trial with strawberry at a dose of 2 g/L limed peat. A very positive and significant effect on Botrytis cinerea disease suppression in the leaves was found for the reference chitin, M4 and R200 compared to the unamended control. The disease suppression of the 3 chitin sources was linked with an increase of the microbial biomass in the limed peat with 24% to 28% due to chitin decomposition and a 9-44% higher N uptake in the plants.

Sustainable Agriculture Systems in Vegetable Production Using Chitin and Chitosan as Plant Biostimulants

Chitin and chitosan are natural compounds that are biodegradable and nontoxic and have gained noticeable attention due to their effective contribution to increased yield and agro-environmental sustainability. Several effects have been reported for chitosan application in plants. Particularly, it can be used in plant defense systems against biological and environmental stress conditions and as a plant growth promoter—it can increase stomatal conductance and reduce transpiration or be applied as a coating material in seeds. Moreover, it can be effective in promoting chitinolytic microorganisms and prolonging storage life through post-harvest treatments, or benefit nutrient delivery to plants since it may prevent leaching and improve slow release of nutrients in fertilizers. Finally, it can remediate polluted soils through the removal of cationic and anionic heavy metals and the improvement of soil properties. On the other hand, chitin also has many beneficial effects such as plant growth promotion, improved plant nutrition and ability to modulate and improve plants’ resistance to abiotic and biotic stressors. The present review presents a literature overview regarding the effects of chitin, chitosan and derivatives on horticultural crops, highlighting their important role in modern sustainable crop production; the main limitations as well as the future prospects of applications of this particular biostimulant category are also presented.

Chitin in Strawberry Cultivation: Foliar Growth and Defense Response Promotion, but Reduced Fruit Yield and Disease Resistance by Nutrient Imbalances

Strawberry cultivation is associated with high mineral fertilizer doses and extensive use of chemical plant protection products. Based on previous research, we expected that chitin application to peat substrate would increase the nutrient availability and activate the plant systemic defense response, resulting in higher strawberry yields and fewer disease symptoms. We set up two experiments in which the temporal variability and differences in initial nutrient concentrations of the growing media were taken into account. Chitin treatment resulted in the attraction of plant growth-promoting fungi toward the plant root, such as species from genera Mortierella and Umbelopsis. In addition, by the end of the experiments 87 mg of mineral nitrogen (N) per liter of substrate was mineralized, which can be related to the observed increase in plant shoot biomass. This, however, led to nutrient imbalances in plant shoots and fruit; N concentration in the leaves increased over 30%, exceeding the optimal range, while phosphorous (P) and potassium (K) deficiencies occurred, with concentrations lower than 50% of the optimal range. This may explain the decreased fruit yield and disease resistance of the fruit toward Botrytis cinerea. In contrast, chitin caused a clear defense priming effect in the strawberry leaves, with a strong induction of the jasmonic acid response, resulting in fewer foliar disease symptoms. Chitin causes positive effects on shoot growth and foliar disease resistance, but caution needs to be taken for nutrient imbalances leading to negative influences on root growth, fruit production, and disease susceptibility toward B. cinerea.[Formula: see text] Copyright © 2021 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license.

Development and Analysis of a Stable, Reduced Complexity Model Soil Microbiome

The soil microbiome is central to the cycling of carbon and other nutrients and to the promotion of plant growth. Despite its importance, analysis of the soil microbiome is difficult due to its sheer complexity, with thousands of interacting species. Here, we reduced this complexity by developing model soil microbial consortia that are simpler and more amenable to experimental analysis but still represent important microbial functions of the native soil ecosystem. Samples were collected from an arid grassland soil and microbial communities (consisting mainly of bacterial species) were enriched on agar plates containing chitin as the main carbon source. Chitin was chosen because it is an abundant carbon and nitrogen polymer in soil that often requires the coordinated action of several microorganisms for complete metabolic degradation. Several soil consortia were derived that had tractable richness (30–50 OTUs) with diverse phyla representative of the native soil, including Actinobacteria, Bacteroidetes, Firmicutes, Proteobacteria, and Verrucomicrobia. The resulting consortia could be stored as glycerol or lyophilized stocks at −80°C and revived while retaining community composition, greatly increasing their use as tools for the research community at large. One of the consortia that was particularly stable was chosen as a model soil consortium (MSC-1) for further analysis. MSC-1 species interactions were studied using both pairwise co-cultivation in liquid media and during growth in soil under several perturbations. Co-abundance analyses highlighted interspecies interactions and helped to define keystone species, including Mycobacterium, Rhodococcus, and Rhizobiales taxa. These experiments demonstrate the success of an approach based on naturally enriching a community of interacting species that can be stored, revived, and shared. The knowledge gained from querying these communities and their interactions will enable better understanding of the soil microbiome and the roles these interactions play in this environment.

Bacterial Tomato Pathogen Ralstonia solanacearum Invasion Modulates Rhizosphere Compounds and Facilitates the Cascade Effect of Fungal Pathogen Fusarium solani

Soil-borne pathogen invasions can significantly change the microbial communities of the host rhizosphere. However, whether bacterial Ralstonia solanacearum pathogen invasion influences the abundance of fungal pathogens remains unclear. In this study, we combined high-throughput sequencing, qPCR, liquid chromatography and soil culture experiments to analyze the rhizosphere fungal composition, co-occurrence of fungal communities, copy numbers of functional genes, contents of phenolic acids and their associations in healthy and bacterial wilt-diseased tomato plants. We found that R. solanacearum invasion increased the abundance of the soil-borne pathogen Fusarium solani. The concentrations of three phenolic acids in the rhizosphere soil of bacterial wilt-diseased tomato plants were significantly higher than those in the rhizosphere soil of healthy tomato plants. In addition, the increased concentrations of phenolic acids significantly stimulated F. solani growth in the soil. Furthermore, a simple fungal network with fewer links, nodes and hubs (highly connected nodes) was found in the diseased tomato plant rhizosphere. These results indicate that once the symptom of bacterial wilt disease is observed in tomato, the roots of the wilt-diseased tomato plants need to be removed in a timely manner to prevent the enrichment of other fungal soil-borne pathogens. These findings provide some ecological clues for the mixed co-occurrence of bacterial wilt disease and other fungal soil-borne diseases.

Myxobacterial Response to Methyljasmonate Exposure Indicates Contribution to Plant Recruitment of Micropredators

Chemical exchanges between plants and microbes within rhizobiomes are critical to the development of community structure. Volatile root exudates such as the phytohormone methyljasmonate (MeJA) contribute to various plant stress responses and have been implicated to play a role in the maintenance of microbial communities. Myxobacteria are competent predators of plant pathogens and are generally considered beneficial to rhizobiomes. While plant recruitment of myxobacteria to stave off pathogens has been suggested, no involved chemical signaling processes are known. Herein we expose predatory myxobacteria to MeJA and employ untargeted mass spectrometry, motility assays, and RNA sequencing to monitor changes in features associated with predation such as specialized metabolism, swarm expansion, and production of lytic enzymes. From a panel of four myxobacteria, we observe the most robust metabolic response from plant-associated Archangium sp. strain Cb G35 with 10 μM MeJA impacting the production of at least 300 metabolites and inducing a ≥ fourfold change in transcription for 56 genes. We also observe that MeJA induces A. sp. motility supporting plant recruitment of a subset of the investigated micropredators. Provided the varying responses to MeJA exposure, our observations indicate that MeJA contributes to the recruitment of select predatory myxobacteria suggesting further efforts are required to explore the microbial impact of plant exudates associated with biotic stress.