Organic farming increases richness of fungal taxa in the wheat phyllosphere

The Effect of Organic and Conventional Cultivation Systems on the Profile of Volatile Organic Compounds in Winter Wheat Grain, Including Susceptibility to Fusarium Head Blight

The grain of 30 winter wheat cultivars differing in terms of their resistance to FHB (Fusarium head blight) was tested. The cultivars were grown in four variants of field trials established in a split-plot design: control without fungicides, chemical control of FHB with fungicides after Fusarium inoculation, Fusarium head inoculation, and organic cultivation. The profile of volatile compounds in grain samples was determined by mean headspace-solid phase microextraction and analyzed by gas chromatography time-of-flight mass spectroscopy. The identified volatile profile comprised 146 compounds belonging to 14 chemical groups. The lowest abundance of volatile organic compounds (VOCs) was found for the organic cultivation variant. The performed discriminant analysis facilitated the complete separation of grain for individual experimental variants based on the number of VOCs decreasing from 116 through 62, 37 down to 14. The grain from organic farming was characterized by a significantly different VOCs profile than the grain from the other variants of the experiment. The compounds 1-methylcycloheptanol, 2-heptanone, 2(3H)-furanone, and 5-hexyldihydro-2(3H)-furanone showed statistically significant differences between all four experimental variants.

Response of microbial communities in the phyllosphere ecosystem of tobacco exposed to the broad-spectrum copper hydroxide

Copper hydroxide is a broad-spectrum copper fungicide, which is often used to control crop fungal and bacterial diseases. In addition to controlling targeted pathogens, copper hydroxide may also affect other non-targeted microorganisms in the phyllosphere ecosystem. At four time points (before spraying, and 5, 10 and 15 days after fungicide application), the response of diseased and healthy tobacco phyllosphere microorganisms to copper hydroxide stress was studied by using Illumina high-throughput sequencing technology, and Biolog tools. The results showed that the microbiome communities of the healthy group were more affected than the disease group, and the fungal community was more sensitive than the bacterial community. The most common genera in the disease group were Alternaria, Boeremia, Cladosporium, Pantoea, Ralstonia, Pseudomonas, and Sphingomonas; while in the healthy group, these were Alternaria, Cladosporium, Symmetrospora, Ralstonia, and Pantoea. After spraying, the alpha diversity of the fungal community decreased at 5 days for both healthy and diseased groups, and then showed an increasing trend, with a significant increase at 15 days for the healthy group. The alpha diversity of bacterial community in healthy and diseased groups increased at 15 days, and the healthy group had a significant difference. The relative abundance of Alternaria and Cladosporium decreased while that of Boeremia, Stagonosporopsis, Symmetrospora, Epicoccum and Phoma increased in the fungal communities of healthy and diseased leaves. The relative abundance of Pantoea decreased first and then increased, while that of Ralstonia, Pseudomonas and Sphingomonas increased first and then decreased in the bacterial communities of healthy and diseased leaves. While copper hydroxide reduced the relative abundance of pathogenic fungi Alternaria and Cladosporium, it also resulted in the decrease of beneficial bacteria such as Actinomycetes and Pantoea, and the increase of potential pathogens such as Boeremia and Stagonosporopsis. After treatment with copper hydroxide, the metabolic capacity of the diseased group improved, while that of the healthy group was significantly suppressed, with a gradual recovery of metabolic activity as the application time extended. The results revealed changes in microbial community composition and metabolic function of healthy and diseased tobacco under copper hydroxide stress, providing a theoretical basis for future studies on microecological protection of phyllosphere.

Organic Farming Allows Balanced Fungal and Oomycetes Communities

Conventional and organic farming systems affect soils differently, thereby influencing microbial diversity and composition. Organic farming, which relies on natural processes, biodiversity, and cycles adapted to local conditions, is generally known to improve soil texture and alleviate microbial diversity loss compared with that of conventional farming, which uses synthetic inputs such as chemical fertilisers, pesticides, and herbicides. Although they affect the health and productivity of host plants, the community dynamics of fungi and fungi-like oomycetes (under Chromista) in organic farmland are poorly understood. The present study aimed to determine the differences in the diversity and composition of fungi and oomycetes inhabiting organic and conventional farm soils using culture-based DNA barcoding and culture-independent environmental DNA (eDNA) metabarcoding. Four tomato farms with different farming practices were selected and investigated: mature pure organic (MPO) via non-pesticide and organic fertiliser, mature integrated organic (MIO) via non-pesticide and chemical fertiliser, mature conventional chemical (MCC) via both pesticide and chemical fertiliser, and young conventional chemical (YCC). Culture-based analysis revealed that different genera were dominant on the four farms: Linnemannia in MPO, Mucor in MIO, and Globisporangium in MCC and YCC. eDNA metabarcoding demonstrated that the fungal richness and diversity on the MPO farm were higher than that on other farms. Both conventional farms exhibited simpler fungal and oomycete network structures with lower phylogenetic diversity. Interestingly, a high richness of oomycetes was shown in YCC; in which, Globisporangium, a potential pathogenic group on tomato plants, was abundantly observed. Our findings indicate that organic farming enhances fungal and oomycete diversity, which may provide robust support for maintaining healthy and sustainable agricultural practices. This study contributes to our knowledge on the positive effects of organic farming on crop microbiomes and provides essential information for maintaining biological diversity.

Constellation of the endophytic mycobiome in spring and winter wheat cultivars grown under various conditions

The mycobiome is an integral component of every living organism. Among other fungi associated with plants, endophytes are an interesting and favorable group of microorganisms, but information regarding them is still largely unknown. Wheat is the most economically significant and essential crop for global food security, which is exposed to a range of abiotic and biotic stresses. Profiling plants' mycobiomes can help in sustainable, chemical-reducing wheat production. The main objective of this work is to understand the structure of endogenous fungal communities in winter and spring wheat cultivars growing under different growth conditions. Further, the study attempted to investigate the effect of host genotype, host organs and plant growth conditions on the composition and distribution of fungi in wheat plant tissues. Comprehensive, high throughput analyzes of the diversity and community structure of the wheat mycobiome were performed, complemented by the simultaneous isolation of endophytic fungi, resulting in candidate strains for future research. The findings of the study revealed that the type of plant organs and growth conditions influence the wheat mycobiome. It was also assessed that fungi representing the genera Cladosporium, Penicillium, and Sarocladium form the core mycobiome of Polish spring and winter wheat cultivars. The coexistence of both symbiotic and pathogenic species in the internal tissues of wheat was also observed. Those commonly considered beneficial for plants can be used in further research as a valuable source of potential biological control factors and/or biostimulators of wheat plant growth.

Composition and variability of core phyllosphere fungal mycobiota on field-grown broccoli

BACKGROUND

Fresh vegetables harbor an assemblage of different microorganisms on their surfaces. The phyllosphere microbiota is important for maintaining plant health and managing crop quality before and after harvest. However, the diversity and ecology of fungal communities are largely unexplored in fresh vegetables. This study investigated the phyllosphere mycobiota of field-grown broccoli florets (n = 66) collected from 22 farms across four regions in Korea, using culturing, amplicon sequencing of the internal transcribed spacer region, and microbial network analysis.

RESULTS

Microbial network analysis identified core genera (Purpureocillium, Filobasidium, Cystofilobasidium, Papiliotrema, Aureobasidium, and unclassified genera of Capnodiales) specific to the broccoli phyllosphere. The composition and network complexity of core and unique populations varied among farming regions, and was associated with local agro-meteorological conditions. The complexity of microbial associations was higher in mature communities than in immature communities, but complexity was lost upon development of plant pathogenic disease. Broccoli mycobiota were classified according to the dominance of Purpurecillium. While Purpurecillium-type microbiota were prevalent in normal samples, Filobasidium-type microbiota were frequently observed in immature, damaged, or postharvest samples.

CONCLUSIONS

Together, fungal communities were important components of phyllosphere microbiota on fresh vegetables, and have substantial potential for exploitation to enhance and stabilize plant health and growth.

Microbiomes in agroecosystem: Diversity, function and assembly mechanisms

Soils are a main repository of biodiversity harbouring immense diversity of microbial species that plays a central role in fundamental ecological processes and acts as the seed bank for emergence of the plant microbiome in cropland ecosystems. Crop-associated microbiomes play an important role in shaping plant performance, which includes but not limited to nutrient uptake, disease resistance, and abiotic stress tolerance. Although our understanding of structure and function of soil and plant microbiomes has been rapidly advancing, most of our knowledge comes from ecosystems in natural environment. In this review, we present an overview of the current knowledge of diversity and function of microbial communities along the soil-plant continuum in agroecosystems. To characterize the ecological mechanisms for community assembly of soil and crop microbiomes, we explore how crop host and environmental factors such as plant species and developmental stage, pathogen invasion, and land management shape microbiome structure, microbial co-occurrence patterns, and crop-microbiome interactions. Particularly, the relative importance of deterministic and stochastic processes in microbial community assembly is illustrated under different environmental conditions, and potential sources and keystone taxa of the crop microbiome are described. Finally, we highlight a few important questions and perspectives in future crop microbiome research.

High-quality genome of the basidiomycete yeast Dioszegia hungarica PDD-24b-2 isolated from cloud water

The genome of the basidiomycete yeast Dioszegia hungarica strain PDD-24b-2 isolated from cloud water at the summit of puy de Dôme (France) was sequenced using a hybrid PacBio and Illumina sequencing strategy. The obtained assembled genome of 20.98 Mb and a GC content of 57% is structured in 16 large-scale contigs ranging from 90 kb to 5.56 Mb, and another 27.2 kb contig representing the complete circular mitochondrial genome. In total, 8,234 proteins were predicted from the genome sequence. The mitochondrial genome shows 16.2% cgu codon usage for arginine but has no canonical cognate tRNA to translate this codon. Detected transposable element (TE)-related sequences account for about 0.63% of the assembled genome. A dataset of 2,068 hand-picked public environmental metagenomes, representing over 20 Tbp of raw reads, was probed for D. hungarica related ITS sequences, and revealed worldwide distribution of this species, particularly in aerial habitats. Growth experiments suggested a psychrophilic phenotype and the ability to disperse by producing ballistospores. The high-quality assembled genome obtained for this D. hungarica strain will help investigate the behavior and ecological functions of this species in the environment.

Spatio-Temporal Variation in the Phyllospheric Microbial Biodiversity of Alternaria Alternata-Infected Tobacco Foliage

Phyllospheric microbial composition of tobacco (Nicotiana tabacum L.) is contingent upon certain factors, such as the growth stage of the plant, leaf position, and cultivar and its geographical location, which influence, either directly or indirectly, the growth, overall health, and production of the tobacco plant. To better understand the spatiotemporal variation of the community and the divergence of phyllospheric microflora, procured from healthy and diseased tobacco leaves infected by Alternaria alternata, the current study employed microbe culturing, high-throughput technique, and BIOLOG ECO. Microbe culturing resulted in the isolation of 153 culturable fungal isolates belonging to 33 genera and 99 bacterial isolates belonging to 15 genera. High-throughput sequencing revealed that the phyllosphere of tobacco was dominantly colonized by Ascomycota and Proteobacteria, whereas, the most abundant fungal and bacterial genera were Alternaria and Pseudomonas. The relative abundance of Alternaria increased in the upper and middle healthy groups from the first collection time to the third, whereas, the relative abundance of Pseudomonas, Sphingomonas, and Methylobacterium from the same positions increased during gradual leaf aging. Non-metric multi-dimensional scaling (NMDs) showed clustering of fungal communities in healthy samples, while bacterial communities of all diseased and healthy groups were found scattered. FUNGuild analysis, from the first collection stage to the third one in both groups, indicated an increase in the relative abundance of Pathotroph-Saprotroph, Pathotroph-Saprotroph-Symbiotroph, and Pathotroph-Symbiotroph. Inclusive of all samples, as per the PICRUSt analysis, the predominant pathway was metabolism function accounting for 50.03%. The average values of omnilog units (OUs) showed relatively higher utilization rates of carbon sources by the microbial flora of healthy leaves. According to the analysis of genus abundances, leaf growth and leaf position were the important drivers of change in structuring the microbial communities. The current findings revealed the complex ecological dynamics that occur in the phyllospheric microbial communities over the course of a spatiotemporal varying environment with the development of tobacco brown spots, highlighting the importance of community succession.

Impacts of global change on the phyllosphere microbiome

Plants form complex interaction networks with diverse microbiomes in the environment, and the intricate interplay between plants and their associated microbiomes can greatly influence ecosystem processes and functions. The phyllosphere, the aerial part of the plant, provides a unique habitat for diverse microbes, and in return the phyllosphere microbiome greatly affects plant performance. As an open system, the phyllosphere is subjected to environmental perturbations, including global change, which will impact the crosstalk between plants and their microbiomes. In this review, we aim to provide a synthesis of current knowledge of the complex interactions between plants and the phyllosphere microbiome under global changes and to identify future priority areas of research on this topic.

Fungi Inhabiting the Wheat Endosphere

Wheat production is influenced by changing environmental conditions, including climatic conditions, which results in the changing composition of microorganisms interacting with this cereal. The group of these microorganisms includes not only endophytic fungi associated with the wheat endosphere, both pathogenic and symbiotic, but also those with yet unrecognized functions and consequences for wheat. This paper reviews the literature in the context of the general characteristics of endophytic fungi inhabiting the internal tissues of wheat. In addition, the importance of epigenetic regulation in wheat-fungus interactions is recognized and the current state of knowledge is demonstrated. The possibilities of using symbiotic endophytic fungi in modern agronomy and wheat cultivation are also proposed. The fact that the current understanding of fungal endophytes in wheat is based on a rather small set of experimental conditions, including wheat genotypes, plant organs, plant tissues, plant development stage, or environmental conditions, is recognized. In addition, most of the research to date has been based on culture-dependent methods that exclude biotrophic and slow-growing species and favor the detection of fast-growing fungi. Additionally, only a few reports of studies on the entire wheat microbiome using high-throughput sequencing techniques exist. Conducting comprehensive research on the mycobiome of the endosphere of wheat, mainly in the context of the possibility of using this knowledge to improve the methods of wheat management, mainly the productivity and health of this cereal, is needed.

Analysis of Stored Wheat Grain-Associated Microbiota Reveals Biocontrol Activity among Microorganisms against Mycotoxigenic Fungi

Wheat grains are colonized by complex microbial communities that have the potential to affect seed quality and susceptibility to disease. Some of the beneficial microbes in these communities have been shown to protect plants against pathogens through antagonism. We evaluated the role of the microbiome in seed health: in particular, against mycotoxin-producing fungi. Amplicon sequencing was used to characterize the seed microbiome and determine if epiphytes and endophytes differ in their fungal and bacterial diversity and community composition. We then isolated culturable fungal and bacterial species and evaluated their antagonistic activity against mycotoxigenic fungi. The most prevalent taxa were found to be shared between the epiphytic and endophytic microbiota of stored wheat seeds. Among the isolated bacteria, Bacillus strains exhibited strong antagonistic properties against fungal pathogens with noteworthy fungal load reduction in wheat grain samples of up to a 3.59 log₁₀ CFU/g compared to untreated controls. We also found that a strain of the yeast, Rhodotorula glutinis, isolated from wheat grains, degrades and/or metabolizes aflatoxin B₁, one of the most dangerous mycotoxins that negatively affects physiological processes in animals and humans. The mycotoxin level in grain samples was significantly reduced up to 65% in the presence of the yeast strain, compared to the untreated control. Our study demonstrates that stored wheat grains are a rich source of bacterial and yeast antagonists with strong inhibitory and biodegradation potential against mycotoxigenic fungi and the mycotoxins they produce, respectively. Utilization of these antagonistic microorganisms may help reduce fungal and mycotoxin contamination, and potentially replace traditionally used synthetic chemicals.

Fusarium mycotoxin content and Fusarium species presence in Czech organic and conventional wheat

Deoxynivalenol and zearalenone content and the presence of Fusarium species in organically and conventionally grown wheat harvested in the Czech Republic during 2015-2017 were studied. Mycotoxin contamination was compared using two approaches. The first was based on samples taken from randomly selected farms in individual regions of the Czech Republic, both organic (154 samples) and conventional (330 samples). In the second approach, a sample set of conventional wheat compatible with organic one was formed, with samples paired according to the preceding crop and region of harvest. Using the first approach, mycotoxins were shown to be higher in conventional wheat; however, there was no difference in mycotoxin contamination between organic and conventional wheat using the second approach. Eight wheat samples with mycotoxin content above the EU limits were found, seven for deoxynivalenol (2.1%) and one for zearalenone (0.3%), all of them originated from conventional farming system. Six of them had maize as the preceding crop. The presence of five Fusarium species (Fusarium avenaceum, Fusarium culmorum, Fusarium graminearum, Fusarium poae and Fusarium sporotrichioides) was compared for the compatible wheat sample sets (second approach). The predominant species were found to be F. poae and F. graminearum in both the organic and conventional wheat. Harvest year significantly influenced both the occurrence of the main Fusarium species and the level of mycotoxin contamination. The study confirmed that (a) organic farming system was able to keep mycotoxin contamination of wheat at a low level, (b) in studies on the significance of organic/conventional agricultural practice on mycotoxin levels in cereals, it is important to pay attention to common production and environmental variables.

Comparative Metagenomics Reveals Microbial Signatures of Sugarcane Phyllosphere in Organic Management

Converting conventional farms to organic systems to improve ecosystem health is an emerging trend in recent decades, yet little is explored to what extent and how this process drives the taxonomic diversity and functional capacity of above-ground microbes. This study was, therefore, conducted to investigate the effects of agricultural management, i.e., organic, transition, and conventional, on the structure and function of sugarcane phyllosphere microbial community using the shotgun metagenomics approach. Comparative metagenome analysis exhibited that farming practices strongly influenced taxonomic and functional diversities, as well as co-occurrence interactions of phyllosphere microbes. A complex microbial network with the highest connectivity was observed in organic farming, indicating strong resilient capabilities of its microbial community to cope with the dynamic environmental stressors. Organic farming also harbored genus Streptomyces as the potential keystone species and plant growth-promoting bacteria as microbial signatures, including Mesorhizobium loti, Bradyrhizobium sp. SG09, Lactobacillus plantarum, and Bacillus cellulosilyticus. Interestingly, numerous toxic compound-degrading species were specifically enriched in transition farming, which might suggest their essential roles in the transformation of conventional to organic farming. Moreover, conventional practice diminished the abundance of genes related to cell motility and energy metabolism of phyllosphere microbes, which could negatively contribute to lower microbial diversity in this habitat. Altogether, our results demonstrated the response of sugarcane-associated phyllosphere microbiota to specific agricultural managements that played vital roles in sustainable sugarcane production.

Succession of the fungal endophytic microbiome of wheat is dependent on tissue-specific interactions between host genotype and environment

Fungi living inside plants affect many aspects of plant health, but little is known about how plant genotype influences the fungal endophytic microbiome. However, a deeper understanding of interactions between plant genotype and biotic and abiotic environment in shaping the plant microbiome is of significance for modern agriculture, with implications for disease management, breeding and the development of biocontrol agents. For this purpose, we analysed the fungal wheat microbiome from seed to plant to seeds and studied how different potential sources of inoculum contributed to shaping of the microbiome. We conducted a large-scale pot experiment with related wheat cultivars over one growth-season in two environments (indoors and outdoors) to disentangle the effects of host genotype, abiotic environment (temperature, humidity, precipitation) and fungi present in the seed stock, air and soil on the succession of the endophytic fungal communities in roots, flag leaves and seeds at harvest. The communities were studied with ITS1 metabarcoding and environmental climate factors were monitored during the experimental period. Host genotype, tissue type and abiotic factors influenced fungal communities significantly. The effect of host genotype was mostly limited to leaves and roots, and was location-independent. While there was a clear effect of plant genotype, the relatedness between cultivars was not reflected in the microbiome. For the phyllosphere microbiome, location-dependent weather conditions factors largely explained differences in abundance, diversity, and presence of genera containing pathogens, whereas the root communities were less affected by abiotic factors. Our findings suggest that airborne fungi are the primary inoculum source for fungal communities in aerial plant parts whereas vertical transmission is likely to be insignificant. In summary, our study demonstrates that host genotype, environment and presence of fungi in the environment shape the endophytic fungal community in wheat over a growing season.

Fusarium Head Blight From a Microbiome Perspective

The fungal genus Fusarium causes several diseases in cereals, including Fusarium head blight (FHB). A number of Fusarium species are involved in disease development and mycotoxin contamination. Lately, the importance of interactions between plant pathogens and the plant microbiome has been increasingly recognized. In this review, we address the significance of the cereal microbiome for the development of Fusarium-related diseases. Fusarium fungi may interact with the host microbiome at multiple stages during their life cycles and in different plant organs including roots, stems, leaves, heads, and crop residues. There are interactions between Fusarium and other fungi and bacteria as well as among Fusarium species. Recent studies have provided a map of the cereal microbiome and revealed how different biotic and abiotic factors drive microbiome assembly. This review synthesizes the current understanding of the cereal microbiome and the implications for Fusarium infection, FHB development, disease control, and mycotoxin contamination. Although annual and regional variations in predominant species are significant, much research has focused on Fusarium graminearum. Surveying the total Fusarium community in environmental samples is now facilitated with novel metabarcoding methods. Further, infection with multiple Fusarium species has been shown to affect disease severity and mycotoxin contamination. A better mechanistic understanding of such multiple infections is necessary to be able to predict the outcome in terms of disease development and mycotoxin production. The knowledge on the composition of the cereal microbiome under different environmental and agricultural conditions is growing. Future studies are needed to clearly link microbiome structure to Fusarium suppression in order to develop novel disease management strategies for example based on conservation biological control approaches.

The effect of wheat seedling density on photosynthesis may be associated with the phyllosphere microorganisms

Wheat seedlings are significantly impacted by the presence of bacteria. However, bacteria are unavoidably growing together with wheat. The study aimed to reveal wheat photosynthesis, phyllosphere bacterial community composition, and a shift in the bacterial community following different density treatments in a closed artificial ecosystem. Here, we report the relationship between photosynthesis and bacterial community in wheat seedlings for different planting densities. In this closed artificial ecosystem, a total of 30 phyla were detected, with 17 of them were simultaneously present in four treatments, under high light intensity and carbon dioxide growth environment. The key phyla detected include Firmicutes, Proteobacteria, and Bacteroidetes. We found that planting densities significantly impacted the photosynthetic characteristics of wheat and bacterial genetic biodiversity, but not on species composition of the bacterial community. Network analysis shows that the phyllosphere bacteria network structures were characterized by the clustering coefficient and modularity. Network for the 1000 plants/m² treatment group exhibits the highest levels of average clustering coefficient but lowest modularity and number of modules, among all plant densities tested. In addition, the network for the 1200 plants/m² treatment group exhibits the best characteristics in terms of net photosynthesis rate and intrinsic water use efficiency, higher complex phyllosphere community network structures, higher abundance of Corynebacterium, and more function of "Amino acid metabolism", which encourages the plants to grow better. The findings presented in this work elucidated the role of plant density in the growth of phyllosphere bacteria during wheat seedlings and provided theoretical support for reasonable wheat density cultivation in closed artificial ecosystems and wheat field production.

It takes three to tango: the importance of microbes, host plant, and soil management to elucidate manipulation strategies for the plant microbiome

The world’s population is expected to grow to almost 10 billion by 2050, placing unprecedented demands on agriculture and natural resources. The risk in food security is also aggravated by climate change and land degradation, which compromise agricultural productivity. In recent years, our understanding of the role of microbial communities on ecosystem functioning, including plant-associated microbes, has advanced considerably. Yet, translating this knowledge into practical agricultural technologies is challenged by the intrinsic complexity of agroecosystems. Here, we review current strategies for plant microbiome manipulation, classifying them into three main pillars: (i) introducing and engineering microbiomes, (ii) breeding and engineering the host plant, and (iii) selecting agricultural practices that enhance resident soil and plant-associated microbial communities. In each of these areas, we analyze current trends in research, as well as research priorities and future perspectives.

Tissue age, orchard location and disease management influence the composition of fungal and bacterial communities present on the bark of apple trees

Plants host microbial communities that can be affected by environmental conditions and agronomic practices. Despite the role of bark as a reservoir of plant pathogens and beneficial microorganisms, no information is available on the effects of disease management on the taxonomic composition of the bark-associated communities of apple trees. We assessed the impact of disease management strategies on fungal and bacterial communities on the bark of a scab-resistant apple cultivar in two orchard locations and for two consecutive seasons. The amplicon sequencing revealed that bark age and orchard location strongly affected fungal and bacterial diversity. Microbiota dissimilarity between orchards evolved during the growing season and showed specific temporal series for fungal and bacterial populations in old and young bark. Disease management did not induce global changes in the microbial populations across locations and seasons, but specifically affected the abundance of some taxa according to bark age, orchard location and sampling time. Therefore, the disease management applied to scab-resistant cultivars, which is based on a limited use of fungicides, partially changed the taxonomic composition of bark-associated fungal and bacterial communities, suggesting the need for a more accurate risk assessment regarding possible pathogen outbreaks.

Fusarium Head Blight Modifies Fungal Endophytic Communities During Infection of Wheat Spikes

Fusarium head blight (FHB) is a devastating disease of wheat heads. It is caused by several species from the genus Fusarium. Several endophytic fungi also colonize wheat spikes asymptomatically. Pathogenic and commensal fungi share and compete for the same niche and thereby influence plant performance. Understanding the natural dynamics of the fungal community and how the pre-established species react to pathogen attack can provide useful information on the disease biology and the potential use of some of these endophytic organisms in disease control strategies. Fungal community composition was assessed during anthesis as well as during FHB attack in wheat spikes during 2016 and 2017 in two locations. Community metabarcoding revealed that endophyte communities are dominated by basidiomycete yeasts before anthesis and shift towards a more opportunistic ascomycete-rich community during kernel development. These dynamics are interrupted when Fusarium spp. colonize wheat spikes. The Fusarium pathogens appear to exclude other fungi from floral tissues as they are associated with a reduction in community diversity, especially in the kernel which they colonize rapidly. Similarly, the presence of several endophytes was negatively correlated with Fusarium spp. and linked with spikes that stayed healthy despite exposure to the pathogen. These endophytes belonged to the genera Cladosporium, Itersonillia and Holtermanniella. These findings support the hypothesis that some naturally occurring endophytes could outcompete or prevent FHB and represent a source of potential biological control agents in wheat.

Performance of Winter Wheat Cultivars Grown Organically and Conventionally with Focus on Fusarium Head Blight and Fusarium Trichothecene Toxins

Growing acreage and changing consumer preferences cause increasing interest in the cereal products originating from organic farming. Lack of results of objective test, however, does not allow drawing conclusions about the effects of cultivation in the organic system and comparison to currently preferred conventional system. Field experiment was conducted in organic and conventional fields. Thirty modern cultivars of winter wheat were sown. They were characterized for disease infection including Fusarium head blight, seed sowing value, the amount of DNA of the six species of Fusarium fungi as well as concentration of ergosterol and trichothecenes in grain. The intensity Fusarium head blight was at a similar level in both systems. However, Fusarium colonization of kernels expressed as ergosterol level or DNA concentration was higher for the organic system. It did not reflect in an increased accumulation of trichothecenes in grain, which was similar in both systems, but sowing value of organically produced seeds was lower. Significant differences between analyzed cropping systems and experimental variants were found. The selection of the individual cultivars for organic growing in terms of resistance to diseases and contamination of grain with Fusarium toxins was possible. Effects of organic growing differ significantly from the conventional and grain obtained such way can be recommended to consumers. There are indications for use of particular cultivars bred for conventional agriculture in the case of organic farming, and the growing organic decreases plant stress resulting from intense fertilization and chemical plant protection.

A Metabarcoding Analysis of the Mycobiome of Wheat Ears Across a Topographically Heterogeneous Field

Plant associated microbial communities have recently received a lot of attention because thought to play a fundamental role in plant health and development. Focusing on cultivated crops, optimized farming practices must consider the role of these communities when aiming at reducing the impact of pathogens and increasing yields. Typical inhabitants of plant’s phyllosphere are bacteria and microscopic fungi, some of them pathogenic for the plant and dangerous for the consumers, due to the production of toxins. In order to efficiently manage the microbiome, the natural drivers regulating community assembly must be clearly understood. In our study we investigated the within field variation of the phyllosphere mycobiome of wheat ears by metabarcoding of the fungal internal transcribed sequence 1 (ITS1). We selected a field characterized by a high topographic heterogeneity, which is reflected in differences in plant productivity and fitness across it. Samples were taken from 30 sampling points laid across the field where data-loggers were placed, measuring the productivity driven under canopy microclimate. The microclimatic conditions were tested as a source of potential environmental variance. Further independent spatial structures were tested using spatial eigenvector maps (MEMs). Results show considerable differences in the phyllosphere composition across the field. The local under canopy environmental conditions at each point were strong predictors of the community composition. Independent spatial effects given by the geographical position of the sampling points showed also a weaker but significant effect. Moreover we observed different spatial responses from different fungal phyla, with results resembling those described in studies done at a regional scale. This study is the first one to investigate the spatial variation of the phyllosphere mycobiome of a commercial crop within the same field. It contributes to the study of the epidemiology and community assembly dynamics of wheat phyllosphere fungi, showing how in-field community variations are the results of different environmental and spatial processes acting simultaneously. It also shows how heterogeneous fields are a smart and useful system to investigate the ecological mechanisms regulating plant microbiome composition.

Interactions and Coadaptation in Plant Metaorganisms

Plants associate with a wide diversity of microorganisms. Some microorganisms engage in intimate associations with the plant host, collectively forming a metaorganism. Such close coexistence with plants requires specific adaptations that allow microorganisms to overcome plant defenses and inhabit plant tissues during growth and reproduction. New data suggest that the plant immune system has a broader role beyond pathogen recognition and also plays an important role in the community assembly of the associated microorganism. We propose that core microorganisms undergo coadaptation with their plant host, notably in response to the plant immune system allowing them to persist and propagate in their host. Microorganisms, which are vertically transmitted from generation to generation via plant seeds, putatively compose highly adapted species and may have plant-beneficial functions. The extent to which plant domestication has impacted the underlying genetics of plant-microbe associations remains poorly understood. We propose that the ability of domesticated plants to select and maintain advantageous microbial partners may have been affected. In this review, we discuss factors that impact plant metaorganism assembly and function. We underline the importance of microbe-microbe interactions in plant tissues, as they are still poorly studied but may have a great impact on plant health.

The tea leaf microbiome shows specific responses to chemical pesticides and biocontrol applications

The plant microbiome is known to be influenced by certain biotic as well as abiotic factors. Nevertheless, the drivers for specific changes in microbial community composition and structure are largely unknown. In the present study, the effects of chemical and biological treatments for plant protection on the indigenous microbiome of Camellia sinensis (L.) Kuntze were contrasted. Assessment of bacteria-specific ribosomal RNA gene fragment amplicons from a representative set of samples showed an increased microbial diversity in treated plants when compared to untreated samples. Moreover, distinct microbial fingerprints were found for plants subjected to a conventional pesticide treatment with lime sulfur as well as for plants that were biologically treated with a Piriformospora indica spore solution. The bacterial community of pesticide-treated plants was augmented by 11 taxa assigned to Proteobacteria and Actinobacteria. In contrast, plants from biological control treatments were augmented by 10 taxa representing a more diversified community enrichment and included members of Actionobacteria, Proteobacteria, Bacteroidetes, Planctomycetes, and Verrucomicrobia. Complementary, molecular quantification of fungi in the samples showed a significantly lower number of internal transcribed spacer copies in plants subjected to biological control treatments, indicating the highest efficiency against fungal pathogens. The overall results show that leaves that are used for tea production show distinct microbiome shifts that are elicited by common pest and pathogen management practices. These shifts in the microbial population indicate non-target effects of the applied treatments.

Euonymus japonicus phyllosphere microbiome is significantly changed by powdery mildew

Euonymus japonicus Thunb. is a woody and ornamental plant popular in China, Europe and North America. Powdery mildew is one of the most serious diseases that affect E. japonicus growth. In this study, the diseased and apparently healthy leaves were collected from E. japonicus planted in a greenbelt in Beijing, and the effect of powdery mildew on the epiphytic microbial community was investigated by using Illumina sequencing. The results showed that the healthy leaves (HL) harbored greater bacterial and fungal diversity than diseased leaves (DL). Furthermore, both bacterial and fungal communities in DL exhibited significantly different structures from those in HL. The relative abundance of several bacterial phyla (Proteobacteria and Firmicutes) and fungal phyla (Ascomycota and Basidiomycota) were altered by powdery mildew. At the genus level, most genera decreased as powdery mildew pathogen Erysiphe increased, while the genera Kocuria and Exiguobacterium markedly increased. Leaf properties, especially protein content was found to significantly affect beta-diversity of the bacterial and fungal community. Network analysis revealed that positive bacterial interactions in DL were stronger than those in HL samples. Insights into the underlying the indigenous microbial phyllosphere populations of E. japonicus response to powdery mildew will help in the development of methods for controlling plant diseases.

Shifts in the Composition of the Microbiota of Stored Wheat Grains in Response to Fumigation

While the wheat-associated microbiome is of major agricultural importance, little is known about the alterations in wheat grain microbial community composition during storage. Characterization of the bacterial and fungal communities in stored wheat grains revealed the impact of phosphine fumigation, one of the most effective methods to eliminate insects in stored commodities, on the composition of the wheat grain microbiome. High-throughput amplicon sequencing of the bacterial 16S rRNA gene and fungal internal transcribed spacer (ITS) region was used to analyze the wheat grain microbiome at different times over as 6 months period of storage. Higher bacterial diversity was found across the samples during the first (immediately after harvest) and second (3 months later) time points, with a predominance of Proteobacteria, Firmicutes, Actinobacteria, Bacteroidetes and Planctomycetes. A two-fold decrease in the number of bacterial operational taxonomic units (OTUs) was observed in wheat grains at the last time point (6 months later), following phosphine treatment. In contrast to the effect of phosphine on bacteria, it did not affect fungal diversity in stored grains. The majority of fungal sequences were assigned to Ascomycota, followed by Basidiomycota, Glomeromycota, and unidentified fungi, which were evenly distributed throughout the storage period. Alpha and beta diversity analyses were confirmed by examination of the cultured microbial taxa obtained from the stored wheat grains. Mycotoxin analysis of wheat grains collected after phosphine fumigation revealed the presence of Fusarium toxins, primarily deoxynivalenol (DON). Several mycotoxigenic Fusarium spp. were also detected in the same samples. Results of the present study indicate that microbiome of stored, whole wheat grains was strongly affected by phosphine fumigation, which changed the structure of the microbial community leading to shifts in species composition toward mycotoxigenic strains. A better understanding of the complex interactions within the microbial communities of stored grains will assist in the development of novel biocontrol strategies to overcome mycotoxin contamination.

Fungicides have complex effects on the wheat phyllosphere mycobiome

Effects of fungicide treatments on non-target fungi in the phyllosphere are not well known. We studied community composition and dynamics of target (Puccinia striiformis) and non-target fungi in wheat that was heavily infected with yellow rust. Mycobiotas in bulk leaf samples and individual leaves were studied by metabarcoding targeting the internal transcribed spacer-1 (ITS1) region of the ribosomal DNA. The amount of yellow rust in individual samples was quantified by qPCR (quantitative PCR). In addition, septoria tritici blotch (Zymoseptoria tritici), powdery mildew (Blumeria graminis), tan spot (Pyrenophora tritici-repentis), and yellow rust (P. striiformis) were visually evaluated. We showed how fungal communities were affected by three different broad-spectrum fungicides that had been applied at different timings and doses to control Puccinia striiformis. We showed that fungal content was relatively constant even after fungicide treatments. Principal component analysis demonstrated that communities from fungicide-treated plots could be separated from the communities in non-treated plots. We observed effects of fungicide treatments on fungal communities using different dose, timing and products. Some fungi, including the target organism P. striiformis were effectively controlled by most of the fungicide applications whereas some yeasts and also P. tritici-repentis increased after treatments. We demonstrated the feasibility of using metabarcoding as a supplement to visual assessments of fungicide effects on target as well as non-target fungi.

Isolation and characterization of culturable endophytic bacterial community of stripe rust-resistant and stripe rust-susceptible Pakistani wheat cultivars

In this study, endophytic bacteria isolated from root, stem, and leaf tissues of stripe rust-susceptible (Inqilab 91, Galaxy 2013, and 15BT023) and stripe rust-resistant (NARC 2011, Ujala 2015, TW1410) cultivars were identified and characterized. Abundance of endophytes was found in roots as compared with stems and leaves. Resistant and susceptible cultivars significantly differed in abundance of endophytic bacteria. Restriction analysis of 16S rRNA genes amplified from 100 bacterial isolates produced 17 unique patterns. Representatives of each of the 17 unique patterns were sequenced and identified. Among the sequenced bacteria, 8 belonged to Firmicutes, 7 were Proteobacteria, and 2 were Actinobacteria. Most of the isolates have plant growth-promoting properties and a few have the potential of producing hydrolytic enzymes. Two isolates showed significant inhibition of rust spore germination. These endophytic bacteria not only can be helpful in growth-promoting activities but also can assist in biocontrol of stripe rust disease.

Human health implications of organic food and organic agriculture: a comprehensive review

This review summarises existing evidence on the impact of organic food on human health. It compares organic vs. conventional food production with respect to parameters important to human health and discusses the potential impact of organic management practices with an emphasis on EU conditions. Organic food consumption may reduce the risk of allergic disease and of overweight and obesity, but the evidence is not conclusive due to likely residual confounding, as consumers of organic food tend to have healthier lifestyles overall. However, animal experiments suggest that identically composed feed from organic or conventional production impacts in different ways on growth and development. In organic agriculture, the use of pesticides is restricted, while residues in conventional fruits and vegetables constitute the main source of human pesticide exposures. Epidemiological studies have reported adverse effects of certain pesticides on children's cognitive development at current levels of exposure, but these data have so far not been applied in formal risk assessments of individual pesticides. Differences in the composition between organic and conventional crops are limited, such as a modestly higher content of phenolic compounds in organic fruit and vegetables, and likely also a lower content of cadmium in organic cereal crops. Organic dairy products, and perhaps also meats, have a higher content of omega-3 fatty acids compared to conventional products. However, these differences are likely of marginal nutritional significance. Of greater concern is the prevalent use of antibiotics in conventional animal production as a key driver of antibiotic resistance in society; antibiotic use is less intensive in organic production. Overall, this review emphasises several documented and likely human health benefits associated with organic food production, and application of such production methods is likely to be beneficial within conventional agriculture, e.g., in integrated pest management.

Spatiotemporal Variation and Networks in the Mycobiome of the Wheat Canopy

The phyllosphere is an important habitat for a diverse microbiome and an important entry point for many pathogens. Factors that shape the phyllosphere microbiome and also the co-existence among members and how they affect disease development are largely understudied. In this study we examined the wheat mycobiome by using metabarcoding of the fungal ITS1 region. Leaf samples were taken from four cultivars grown at two locations in Denmark. Samples were taken from the three uppermost leaves and at three growth stages to better understand spatiotemporal variation of the mycobiome. Analysis of read abundances showed that geographical location had a major effect in shaping the mycobiome in the total dataset, but also leaf position, growth stage and cultivar were important drivers of fungal communities. Cultivar was most important in explaining variation in older leaves whereas location better explained the variation in younger leaves, suggesting that communities are shaped over time by the leaf environment. Network analysis revealed negative co-existence between Zymoseptoria tritici and the yeasts Sporobolomyces, Dioszegia, and Cystofilobasidiaceae. The relative abundance of Z. tritici and the yeasts was relatively constant between individual samples, suggesting that fast growing fungi rapidly occupy empty space in the phyllosphere.