Minimal impacts on the wheat microbiome when Trichoderma gamsii T6085 is applied as a biocontrol agent to manage fusarium head blight disease

The biocontrol agent Streptomyces rimosus subsp. rimosus tempers shifts in the wheat spicosphere microbiome induced by Fusarium Head Blight

Introduction

Fusarium Head Blight (FHB) is a major fungal disease in wheat caused by Fusarium graminearum, inducing severe yield losses. Biological control agents (BCAs) can be an effective and sustainable approach to mitigate this phytopathogen. In this study, Streptomyces rimosus subsp. rimosus LMG19352 was used as a BCA to mitigate F. graminearum on wheat ears. Moreover, we aimed to assess the impact of BCA inoculation on non-target microorganisms present on the wheat spikes. Therefore, we evaluated shifts in the fungal and bacterial spicosphere microbiome (i) over time from flowering to mid-grain filling stage and (ii) across inoculations with F. graminearum and/or S. rimosus subsp. rimosus LMG19352.

Methods

FHB symptoms were determined by multispectral imaging, and Illumina MiSeq was used to amplify 16S V3-V4 rDNA for bacteria and ITS2 for fungi, whereafter a correlation network analysis was performed.

Results

The biocontrol potential of S. rimosus subsp. rimosus LMG19352 against F. graminearum was confirmed, as FHB symptoms were significantly reduced. Based on the microbial abundances, S. rimosus subsp. rimosus LMG19352 compensated for shifts in the spicosphere microbiome community induced by FHB. These results were supported by a network analysis, revealing a more complex and stable microbiome in the presence of the BCA compared to the infected control.

Discussion

To our knowledge, this study is the first to reveal the potential of a bacterial BCA to temper shifts in the wheat microbiome caused by a phytopathogen, and thereby acting as a promising BCA.

Untrimmed ITS2 metabarcode sequences cause artificially reduced abundances of specific fungal taxa

Advances in DNA metabarcoding have greatly expanded our knowledge of microbial communities in recent years. Pipelines and parameters have been tested extensively for bacterial metabarcoding using the 16S rRNA gene and best practices are largely established. For fungal metabarcoding using the internal transcribed spacer (ITS) gene, however, only a few studies have considered how such pipelines and parameters can affect community prediction. Here, we report a novel bias uncovered during ITS region 2 (ITS2) sequencing of Trichoderma-infected ant fungus gardens and confirmed this bias using mock communities. Abnormally low forward read quality caused Trichoderma ITS2 reads to be computationally filtered before and during read pair merging, thus almost entirely eliminating Trichoderma amplicon sequence variants from the resulting fungal community profiles. Sliding window quality trimming before filtering allowed most of these reads to pass filtering and merge successfully, producing community profiles that now correlated with visual signs of Trichoderma infection and matched the composition of the mock communities. Applying such sliding window trimming to a previously generated environmental ITS2 data set increased the detected fungal diversity and again overcame read quality biases against Trichoderma to detect it in nearly every sample instead and often at high relative abundances. This analysis additionally identified a similar, but distinct, bias against a second fungal genus Meyerozyma. The prevalence of such quality biases against other fungal ITS sequences is unknown but may be widespread. We, therefore, advocate for the routine use of sliding window quality trimming as a best practice in ITS2 metabarcoding analysis.

IMPORTANCE

Metabarcode sequencing produces DNA abundance profiles that are presumed to reflect the actual microbial composition of their corresponding input samples. However, this assumption is not always tested, and taxon-specific biases are often not apparent, especially for low-abundance taxa in complex communities. Here, we identified internal transcribed spacer region 2 (ITS2) read quality aberrations that caused dramatic reductions in the relative abundances of specific taxa in multiple data sets characterizing ant fungus gardens. Such taxon-specific biases in read quality may be widespread in other environments and for other fungal taxa, thereby causing incorrect descriptions of these mycobiomes.

The impact of spray-induced gene silencing on cereal phyllosphere microbiota

BACKGROUND

Fusarium head blight (FHB) is a major disease affecting cereal crops including wheat, barley, rye, oats and maize. Its predominant causal agent is the ascomycete fungus Fusarium graminearum, which infects the spikes and thereby reduces grain yield and quality. The frequency and severity of FHB epidemics has increased in recent years, threatening global food security. Spray-induced gene silencing (SIGS) is an alternative technique for tackling this devastating disease through foliar spraying with exogenous double-stranded RNA (dsRNA) to silence specific pathogen genes via RNA interference. This has the advantage of avoiding transgenic approaches, but several aspects of the technology require further development to make it a viable field-level management tool. One such existing knowledge gap is how dsRNA spraying affects the microbiota of the host plants.

RESULTS

We found that the diversity, structure and composition of the bacterial microbiota are subject to changes depending on dsRNA targeted and host studied, while the fungal microbiota in the phyllosphere remained relatively unchanged upon spraying with dsRNA. Analyses of fungal co-occurrence patterns also showed that F. graminearum established itself among the fungal communities through negative interactions with neighbouring fungi. Through these analyses, we have also found bacterial and fungal genera ubiquitous in the phyllosphere, irrespective of dsRNA treatment. These results suggest that although rarer and less abundant microbial species change upon dsRNA spray, the ubiquitous bacterial and fungal components of the phyllosphere in wheat and barley remain unchanged.

CONCLUSION

We show for the first time the effects of exogenous dsRNA spraying on bacterial and fungal communities in the wheat and barley phyllospheres using a high-throughput amplicon sequencing approach. The results obtained further validate the safety and target-specificity of SIGS and emphasize its potential as an environmentally friendly option for managing Fusarium head blight in wheat and barley.

Use in a controlled environment of Trichoderma asperellum ICC012 and Trichoderma gamsii ICC080 to manage FHB on common wheat

Fusarium head blight (FHB) represents a significant threat for wheat production due to the risk for food security and safety. Despite the huge number of biofungicides on the market, only one is actually available at European level to control Fusarium infections on cereals. The present work aimed to assess the possible use of Trichoderma asperellum strain ICC012 and Trichoderma gamsii strain ICC080 to manage FHB on common wheat Triticum aestivum cv Apogee. Initially, the capability of ICC012 and ICC080 to endophytically colonize wheat roots, a prerequisite very often correlated with the induction of resistance in the host plant, was investigated. It resulted in 100 % of roots internally colonized by the two strains, followed by a significant up-regulation of the defense-related genes encoding for pathogenesis-related protein 1 (pr1), superoxide dismutase (sod), polygalacturonase inhibitor protein 2 (pgip2) and phenylalanine ammonia-lyase 1 (pal1). When the expression of the same genes was investigated in spikes treated at the flowering stage with the two strains, applied individually or co-inoculated, a significant up-regulation of only pal1 was registered 24 hours post inoculation (hpi) in spikes treated with ICC080. To check if a systemic defense response was induced, the expression of the same genes was analyzed in leaves collected 7 and 14 days post inoculation (dpi) of roots, resulting in a significant up-regulation of sod at 7 dpi in leaves collected from plants inoculated with ICC012. Even if induction of resistance is probably not the main mode of action of the two strains, ICC012 and ICC080 applied on spikes at anthesis significantly reduced, in greenhouse conditions, the Disease Incidence (DI) caused by the inoculation mix of F. graminearum, F. culmorum, F. langsethiae and F. sporotrichioides, four of the most important FHB casual agents. This reduction in disease symptoms was observed when the two beneficial strains were applied both individually and co-inoculated on the spikes. Finally, ICC012 and ICC080 demonstrated a good competitive ability for substrate possession. The amount of F. graminearum (as DNA and number of perithecia) on wheat straw pieces was significantly reduced after 6 months of incubation in presence of the two beneficial strains, applied individually and co-inoculated. Being cultural debris used to overwinter, this competitive behavior of ICC012 and ICC080 is an important trait to reduce the potential inoculum of the pathogen. The results collected here lay the groundwork for the use of ICC012 and ICC080 in managing FHB on common wheat.

Biodiversity of Trichoderma species of healthy and Fusarium wilt-infected banana rhizosphere soils in Tenerife (Canary Islands, Spain)

Banana (Musa acuminata) is the most important crop in the Canary Islands (38.9% of the total cultivated area). The main pathogen affecting this crop is the soil fungal Fusarium oxysporum f. sp. cubense subtropical race 4 (Foc-STR4), for which there is no effective control method under field conditions. Therefore, the use of native biological control agents may be an effective and sustainable alternative. This study aims to: (i) investigate the diversity and distribution of Trichoderma species in the rhizosphere of different banana agroecosystems affected by Foc-STR4 in Tenerife (the island with the greatest bioclimatic diversity and cultivated area), (ii) develop and preserve a culture collection of native Trichoderma species, and (iii) evaluate the influence of soil chemical properties on the Trichoderma community. A total of 131 Trichoderma isolates were obtained from 84 soil samples collected from 14 farms located in different agroecosystems on the northern (cooler and wetter) and southern (warmer and drier) slopes of Tenerife. Ten Trichoderma species, including T. afroharzianum, T. asperellum, T. atrobrunneum, T. gamsii, T. guizhouense, T. hamatum, T. harzianum, T. hirsutum, T. longibrachiatum, and T. virens, and two putative novel species, named T. aff. harzianum and T. aff. hortense, were identified based on the tef1-α sequences. Trichoderma virens (35.89% relative abundance) and T. aff. harzianum (27.48%) were the most abundant and dominant species on both slopes, while other species were observed only on one slope (north or south). Biodiversity indices (Margalef, Shannon, Simpson, and Pielou) showed that species diversity and evenness were highest in the healthy soils of the northern slope. The Spearman analysis showed significant correlations between Trichoderma species and soil chemistry parameters (mainly with phosphorus and soil pH). To the best of our knowledge, six species are reported for the first time in the Canary Islands (T. afroharzianum, T. asperellum, T. atrobrunneum, T. guizhouense, T. hamatum, T. hirsutum) and in the rhizosphere of banana soils (T. afroharzianum, T. atrobrunneum, T. gamsii, T. guizhouense, T. hirsutum, T. virens). This study provides essential information on the diversity/distribution of native Trichoderma species for the benefit of future applications in the control of Foc-STR4.

Assessment of soil yeasts Papiliotrema laurentii S-08 and Saitozyma podzolica S-77 for plant growth promotion and biocontrol of Fusarium wilt of brinjal

AIM

This study aimed to determine the efficacy of the soil yeasts Papiliotrema laurentii S-08 and Saitozyma podzolica S-77 for plant growth promotion (PGP) and biocontrol of wilt disease in brinjal plants while applying yeasts individually or as a consortium in pot experiments.

METHODS AND RESULTS

The yeasts were tested for various PGP characteristics and antagonistic activity against the phytopathogen Fusarium oxysporum f. sp. melongenae. Both the yeast isolates demonstrated some PGP attributes as well as inhibited the growth of the phytopathogen. A gas chromatography-mass spectrometry analysis of the yeast metabolites revealed the presence of several antifungal compounds. The pot experiment performed under nursery conditions showed that applying these yeasts, individually or in consortium, decreased the percent disease incidence in brinjal seedlings while significantly enhancing their growth parameters.

CONCLUSION

Papiliotrema laurentii S-08 and S. podzolica S-77 can be used in brinjal plants as plant growth promoters and also as biocontrol agents against the brinjal wilt disease.

Trichoderma and its role in biological control of plant fungal and nematode disease

Trichoderma is mainly used to control soil-borne diseases as well as some leaf and panicle diseases of various plants. Trichoderma can not only prevent diseases but also promotes plant growth, improves nutrient utilization efficiency, enhances plant resistance, and improves agrochemical pollution environment. Trichoderma spp. also behaves as a safe, low-cost, effective, eco-friendly biocontrol agent for different crop species. In this study, we introduced the biological control mechanism of Trichoderma in plant fungal and nematode disease, including competition, antibiosis, antagonism, and mycoparasitism, as well as the mechanism of promoting plant growth and inducing plant systemic resistance between Trichoderma and plants, and expounded on the application and control effects of Trichoderma in the control of various plant fungal and nematode diseases. From an applicative point of view, establishing a diversified application technology for Trichoderma is an important development direction for its role in the sustainable development of agriculture.