Crop Management Impacts the Soybean (Glycine max) Microbiome

Accumulation of pathogens in soil microbiome can explain long-term fluctuations of legumes in a grassland community

All plant populations fluctuate in time. Apart from the dynamics imposed by external forces such as climate, these fluctuations can be driven by endogenous processes taking place within the community. In this study, we aimed to identify potential role of soil-borne microbial communities in driving endogenous fluctuations of plant populations. We combined a unique, 35-yr long abundance data of 11 common plant species from a species-rich mountain meadow with development of their soil microbiome (pathogenic fungi, arbuscular mycorrhizal fungi and oomycetes) observed during 4 yr of experimental cultivation in monocultures. Plant species which abundance fluctuated highly in the field (particularly legumes) accumulated plant pathogens in their soil mycobiome. We also identified increasing proportion of mycoparasitic fungi under highly fluctuating legume species, which may indicate an adaptation of these species to mitigate the detrimental effects of pathogens. Our study documented that long-term fluctuations in the abundance of plant species in grassland communities can be explained by the accumulation of plant pathogens in plant-soil microbiome. By contrast, we found little evidence of the role of mutualists in plant population fluctuations. These findings offer new insights for understanding mechanisms driving both long-term vegetation dynamics and patterns of species coexistence and richness.

Fine-scale characterization of the soybean rhizosphere microbiome via synthetic long reads and avidity sequencing

BACKGROUND

The rhizosphere microbiome displays structural and functional dynamism driven by plant, microbial, and environmental factors. While such plasticity is a well-evidenced determinant of host health, individual and community-level microbial activity within the rhizosphere remain poorly understood, due in part to the insufficient taxonomic resolution achieved through traditional marker gene amplicon sequencing. This limitation necessitates more advanced approaches (e.g., long-read sequencing) to derive ecological inferences with practical application. To this end, the present study coupled synthetic long-read technology with avidity sequencing to investigate eukaryotic and prokaryotic microbiome dynamics within the soybean (Glycine max) rhizosphere under field conditions.

RESULTS

Synthetic long-read sequencing permitted de novo reconstruction of the entire 18S-ITS1-ITS2 region of the eukaryotic rRNA operon as well as all nine hypervariable regions of the 16S rRNA gene. All full-length, mapped eukaryotic amplicon sequence variants displayed genus-level classification, and 44.77% achieved species-level classification. The resultant eukaryotic microbiome encompassed five kingdoms (19 genera) of protists in addition to fungi - a depth unattainable with conventional short-read methods. In the prokaryotic fraction, every full-length, mapped amplicon sequence variant was resolved at the species level, and 23.13% at the strain level. Thirteen species of Bradyrhizobium were thereby distinguished in the prokaryotic microbiome, with strain-level identification of the two Bradyrhizobium species most reported to nodulate soybean. Moreover, the applied methodology delineated structural and compositional dynamism in response to experimental parameters (i.e., growth stage, cultivar, and biostimulant application), unveiled a saprotroph-rich core microbiome, provided empirical evidence for host selection of mutualistic taxa, and identified key microbial co-occurrence network members likely associated with edaphic and agronomic properties.

CONCLUSIONS

This study is the first to combine synthetic long-read technology and avidity sequencing to profile both eukaryotic and prokaryotic fractions of a plant-associated microbiome. Findings herein provide an unparalleled taxonomic resolution of the soybean rhizosphere microbiota and represent significant biological and technological advancements in crop microbiome research.

Impact of Foliar Fungicide Application on the Culturable Fungal Endophyte Community of Soybean Seed in the Midwest United States

The purpose of our study was to determine whether the application of quinone outside inhibitor (QoI) and pyrazole-carboxamide fungicides as a tank mix would impact the endophyte community of soybean seed. Field trials during 2018 in Iowa, South Dakota, and Wisconsin, U.S.A., investigated the impact of a single combination fungicide spray at early pod set in soybeans. The composition of culturable endophytic fungi in mature soybean seed was assessed on three cultivars per state, with maturity groups (MGs) ranging from 1.1 to 4.7. An unusually wet 2018 season delayed harvest, which led to a high level of fungal growth in grain. The survey included 1,080 asymptomatic seeds that were disinfested and individually placed on 5-cm-diameter Petri plates of acidified water agar. The survey yielded 721 fungal isolates belonging to 24 putative species in seven genera; taxa were grouped into genera based on a combination of morphological and molecular evidence. The dominant genera encountered in the survey were Alternaria, Diaporthe, and Fusarium. The study showed that the fungicide treatment reduced the incidence of Fusarium in Wisconsin seed, increased the incidence of Diaporthe in seed from all states, and had no impact on the incidence of Alternaria. This is one of the first attempts to characterize the diversity of seed endophytes in soybean and the first to characterize the impacts of fungicide spraying on these endophyte communities across three states. Our study provides evidence that the impact of a fungicide spray on soybean seed endophyte communities may be influenced by site, weather, and cultivar maturity group.

Microbiome structure variation and soybean's defense responses during flooding stress and elevated CO2

Introduction

With current trends in global climate change, both flooding episodes and higher levels of CO2 have been key factors to impact plant growth and stress tolerance. Very little is known about how both factors can influence the microbiome diversity and function, especially in tolerant soybean cultivars. This work aims to (i) elucidate the impact of flooding stress and increased levels of CO2 on the plant defenses and (ii) understand the microbiome diversity during flooding stress and elevated CO2 (eCO2).

Methods

We used next-generation sequencing and bioinformatic methods to show the impact of natural flooding and eCO2 on the microbiome architecture of soybean plants' below- (soil) and above-ground organs (root and shoot). We used high throughput rhizospheric extra-cellular enzymes and molecular analysis of plant defense-related genes to understand microbial diversity in plant responses during eCO2 and flooding.

Results

Results revealed that bacterial and fungal diversity was substantially higher in combined flooding and eCO2 treatments than in non-flooding control. Microbial diversity was soil>root>shoot in response to flooding and eCO2. We found that sole treatment of eCO2 and flooding had significant abundances of Chitinophaga, Clostridium, and Bacillus. Whereas the combination of flooding and eCO2 conditions showed a significant abundance of Trichoderma and Gibberella. Rhizospheric extra-cellular enzyme activities were significantly higher in eCO2 than flooding or its combination with eCO2. Plant defense responses were significantly regulated by the oxidative stress enzyme activities and gene expression of Elongation factor 1 and Alcohol dehydrogenase 2 in floodings and eCO2 treatments in soybean plant root or shoot parts.

Conclusion

This work suggests that climatic-induced changes in eCO2 and submergence can reshape microbiome structure and host defenses, essential in plant breeding and developing stress-tolerant crops. This work can help in identifying core-microbiome species that are unique to flooding stress environments and increasing eCO2.

Update on the state of research to manage Fusarium head blight

Fusarium head blight (FHB) is one of the most devastating diseases of cereal crops, causing severe reduction in yield and quality of grain worldwide. In the United States, the major causal agent of FHB is the mycotoxigenic fungus, Fusarium graminearum. The contamination of grain with mycotoxins, including deoxynivalenol and zearalenone, is a particularly serious concern due to its impact on the health of humans and livestock. For the past few decades, multidisciplinary studies have been conducted on management strategies designed to reduce the losses caused by FHB. However, effective management is still challenging due to the emergence of fungicide-tolerant strains of F. graminearum and the lack of highly resistant wheat and barley cultivars. This review presents multidisciplinary approaches that incorporate advances in genomics, genetic-engineering, new fungicide chemistries, applied biocontrol, and consideration of the disease cycle for management of FHB.

Characterizing microbial communities associated with northern root-knot nematode (Meloidogyne hapla) occurrence and soil health

The northern root-knot nematode (Meloidogyne hapla) causes extensive damage to agricultural crops globally. In addition, M. hapla populations with no known genetic or morphological differences exhibit parasitic variability (PV) or reproductive potential based on soil type. However, why M. hapla populations from mineral soil with degraded soil health conditions have a higher PV than populations from muck soil is unknown. To improve our understanding of soil bio-physicochemical conditions in the environment where M. hapla populations exhibited PV, this study characterized the soil microbial community and core- and indicator-species structure associated with M. hapla occurrence and soil health conditions in 15 Michigan mineral and muck vegetable production fields. Bacterial and fungal communities in soils from where nematodes were isolated were characterized with high throughput sequencing of 16S and internal transcribed spacer (ITS) rDNA. Our results showed that M. hapla-infested, as well as disturbed and degraded muck fields, had lower bacterial diversity (observed richness and Shannon) compared to corresponding mineral soil fields or non-infested mineral fields. Bacterial and fungal community abundance varied by soil group, soil health conditions, and/or M. hapla occurrence. A core microbial community was found to consist of 39 bacterial and 44 fungal sub-operational taxonomic units (OTUs) across all fields. In addition, 25 bacteria were resolved as indicator OTUs associated with M. hapla presence or absence, and 1,065 bacteria as indicator OTUs associated with soil health conditions. Out of the 1,065 bacterial OTUs, 73.9% indicated stable soil health, 8.4% disturbed, and 0.4% degraded condition; no indicators were common to the three categories. Collectively, these results provide a foundation for an in-depth understanding of the environment where M. hapla exists and conditions associated with parasitic variability.

Soybean and Cotton Spermosphere Soil Microbiome Shows Dominance of Soilborne Copiotrophs

The spermosphere is the transient, immediate zone of soil around imbibing and germinating seeds. It represents a habitat where there is contact between seed-associated microbes and soil microbes, but it is studied less than other plant habitats. Previous studies on spermosphere microbiology were primarily culture based or did not sample the spermosphere soil as initially defined in space and time. Thus, the objectives of this study were to develop an efficient strategy to collect spermosphere soils around imbibing soybean and cotton in nonsterile soil and investigate changes in microbial communities. The method employed sufficiently collected spermosphere soil as initially defined in space by constraining the soil sampled with a cork borer and confining the soil to a 12-well microtiter plate. Spermosphere prokaryote composition changed over time and depended on the crop within 6 h after seeds were sown. By 12 to 18 h, crops had unique microbial communities in spermosphere soils. Prokaryote evenness dropped following seed imbibition, with the proliferation of copiotrophic soil bacteria. Due to their long history of plant growth promotion, prokaryote operational taxonomic units (OTUs) in Bacillus, Paenibacillus, Burkholderia, Massilia, Azospirillum, and Pseudomonas were notable organisms enriched. Fungi and prokaryotes were hub taxa in cotton and soybean spermosphere networks. Additionally, the enriched taxa were not hubs in networks, suggesting that other taxa besides those enriched may be important for spermosphere communities. Overall, this study advances knowledge in the assembly of the plant microbiome early in a plant's life, which may have plant health implications in more mature plant growth stages. IMPORTANCE The central hypothesis of this research was that plant species and seed exudate release would alter the assembly of microbes in the spermosphere soil. Our research investigated the response of microbes to the initial burst of nutrients into the spermosphere soil, filling knowledge gaps from previous studies that pregerminated seeds under sterile conditions. We identified several copiotrophic bacterial lineages with a long history of plant growth promotion proliferating in response to the initial exudate release. With a comparative network approach, we show that these copiotrophic bacteria are not central to networks, demonstrating that other microbes (including fungi) may be important for community structure. This study improves knowledge on microbial dynamics in the understudied spermosphere and helps inform solutions for biologically or ecologically motivated solutions to spermosphere pathogens.

Biodiversity of Endophytic Microbes in Diverse Tea Chrysanthemum Cultivars and Their Potential Promoting Effects on Plant Growth and Quality

The endophytic microbiomes significantly differed across tea chrysanthemum cultivars and organs (stems and leaves). The most abundant endophytic bacterial genera were Pseudomonas, Masillia, and Enterobacter in the leaves and Sphingomonas and Curtobacterium in the stems of the five cultivars. Meanwhile, the most abundant endophytic fungal genera in the leaves and stems of the five tea chrysanthemums were Alternaria, Cladosporium, and Sporobolomyces. Specifically, Rhodotorula was dominant in the leaves of 'Jinsi huangjv' and Paraphoma was dominant in the stems of 'Jinsi huangjv'. In all cultivars, the diversity and richness of endophytic bacteria were higher in leaves than in stems (p < 0.05). The highest diversity and richness of endophytic bacteria were recorded in 'Chujv', followed by 'Jinsi huangjv', 'Fubai jv', 'Nannong jinjv', and 'Hangbai jv'. Meanwhile, endophytic fungi were less pronounced. Twenty-seven and 15 cultivable endophytic bacteria and fungi were isolated, four isolated endophytic bacteria, namely, CJY1 (Bacillus oryzaecorticis), CY2 (Pseudomonas psychrotolerans), JSJ7, and JSJ17 (Enterobacter cloacae) showed higher indole acetic acid production ability. Further field studies indicated that inoculation of these four endophytic bacteria not only promoted plant growth and yield but also increased total flavonoids, chlorogenic acid, luteolin, and 3,5-dicoffeylquinic acid levels in the dry flowers of tea chrysanthemums.

Regional biogeography versus intra-annual dynamics of the root and soil microbiome

BACKGROUND

Root and soil microbial communities constitute the below-ground plant microbiome, are drivers of nutrient cycling, and affect plant productivity. However, our understanding of their spatiotemporal patterns is confounded by exogenous factors that covary spatially, such as changes in host plant species, climate, and edaphic factors. These spatiotemporal patterns likely differ across microbiome domains (bacteria and fungi) and niches (root vs. soil).

RESULTS

To capture spatial patterns at a regional scale, we sampled the below-ground microbiome of switchgrass monocultures of five sites spanning > 3 degrees of latitude within the Great Lakes region. To capture temporal patterns, we sampled the below-ground microbiome across the growing season within a single site. We compared the strength of spatiotemporal factors to nitrogen addition determining the major drivers in our perennial cropping system. All microbial communities were most strongly structured by sampling site, though collection date also had strong effects; in contrast, nitrogen addition had little to no effect on communities. Though all microbial communities were found to have significant spatiotemporal patterns, sampling site and collection date better explained bacterial than fungal community structure, which appeared more defined by stochastic processes. Root communities, especially bacterial, were more temporally structured than soil communities which were more spatially structured, both across and within sampling sites. Finally, we characterized a core set of taxa in the switchgrass microbiome that persists across space and time. These core taxa represented < 6% of total species richness but > 27% of relative abundance, with potential nitrogen fixing bacteria and fungal mutualists dominating the root community and saprotrophs dominating the soil community.

CONCLUSIONS

Our results highlight the dynamic variability of plant microbiome composition and assembly across space and time, even within a single variety of a plant species. Root and soil fungal community compositions appeared spatiotemporally paired, while root and soil bacterial communities showed a temporal lag in compositional similarity suggesting active recruitment of soil bacteria into the root niche throughout the growing season. A better understanding of the drivers of these differential responses to space and time may improve our ability to predict microbial community structure and function under novel conditions.

Characterization of Boxwood Shoot Bacterial Communities and Potential Impact from Fungicide Treatments

Phyllosphere bacterial communities play important roles in plant fitness and growth. The objective of this study was to characterize the epiphytic and endophytic bacterial communities of boxwood shoots and determine how they may respond to commonly used fungicides. In early summer and early fall, shoot samples were collected immediately before and 1, 7, and 14 days after three fungicides containing chlorothalonil and/or propiconazole were applied to the canopy. Total genomic DNA from shoot surface washings and surface-sterilized shoot tissues was used as the template for 16S rRNA metabarcoding, and the amplicons were sequenced on a Nanopore MinION sequencer to characterize the epiphytic and endophytic communities. The bacterial communities were phylogenetically more diverse on the boxwood shoot surface than in the internal tissue, although the two communities shared 12.7% of the total 1,649 identified genera. The most abundant epiphytes were Methylobacterium and Pantoea, while Stenotrophomonas and Brevundimonas were the dominant endophytes. Fungicide treatments had strong impacts on epiphytic bacterial community structure and composition. Analysis of compositions of microbiomes with bias correction (ANCOM-BC) and analysis of variance (ANOVA)-like differential expression (ALDEx2) together identified 312 and 1,362 epiphytes changed in abundance due to fungicide treatments in early summer and early fall, respectively, and over 50% of these epiphytes were negatively impacted by fungicide. The two chlorothalonil-based contact fungicides demonstrated more marked effects than the propiconazole-based systemic fungicide. These results are foundational for exploring and utilizing the full potential of the microbiome and fungicide applications and developing a systems approach to boxwood health and production. IMPORTANCE Agrochemicals are important tools for safeguarding plants from invasive pathogens, insects, mites, and weeds. How they may affect the plant microbiome, a critical component of crop health and production, was poorly understood. Here, we used boxwood, an iconic low-maintenance landscape plant, to characterize shoot epiphytic and endophytic bacterial communities and their responses to contact and systemic fungicides. This study expanded our understanding of the above-ground microbiome in ornamental plants and is foundational for utilizing the full benefits of the microbiome in concert with different fungicide chemistries to improve boxwood health. This study also sets an example for a more thorough evaluation of these and other agrochemicals for their effects on boxwood microbiomes during production and offers an expanded systems approach that could be used with other crops for enhanced integrated pest management.

Australian native Glycine clandestina seed microbiota hosts a more diverse bacterial community than the domesticated soybean Glycine max

BACKGROUND

Plant microbiome composition has been demonstrated to change during the domestication of wild plants and it is suggested that this has resulted in loss of plant beneficial microbes. Recently, the seed microbiome of native plants was demonstrated to harbour a more diverse microbiota and shared a common core microbiome with modern cultivars. In this study the composition of the seed-associated bacteria of Glycine clandestina is compared to seed-associated bacteria of Glycine max (soybean).

RESULTS

The seed microbiome of the native legume Glycine clandestina (crop wild relative; cwr) was more diverse than that of the domesticated Glycine max and was dominated by the bacterial class Gammaproteobacteria. Both the plant species (cwr vs domesticated) and individual seed accessions were identified as the main driver for this diversity and composition of the microbiota of all Glycine seed lots, with the effect of factor "plant species" exceeded that of "geographical location". A core microbiome was identified between the two Glycine species. A high percentage of the Glycine microbiome was unculturable [G. clandestina (80.8%) and G. max (75.5%)] with only bacteria of a high relative abundance being culturable under the conditions of this study.

CONCLUSION

Our results provided novel insights into the structure and diversity of the native Glycine clandestina seed microbiome and how it compares to that of the domesticated crop Glycine max. Beyond that, it also increased our knowledge of the key microbial taxa associated with the core Glycine spp. microbiome, both wild and domesticated. The investigation of this commonality and diversity is a valuable and essential tool in understanding the use of native Glycine spp. for the discovery of new microbes that would be of benefit to domesticated Glycine max cultivars or any other economically important crops. This study has isolated microbes from a crop wild relative that are now available for testing in G. max for beneficial phenotypes.

Evaluating the Rhizosphere and Endophytic Microbiomes of a Bamboo Plant in Response to the Long-Term Application of Heavy Organic Amendment

Root-associated bacteria play a major role in plant health and productivity. However, how organic amendment influences root-associated bacteria is uncertain in Lei bamboo (Phyllostachys praecox) plantations. Here, we compared the rhizosphere and endophytic microbiomes in two Lei bamboo plantations with (IMS) and without (TMS) the application of organic amendment for 16 years. The results showed IMS significantly increased (p < 0.05) the relative abundance of Proteobacteria and significantly decreased (p < 0.05) the relative abundance of Acidobacteria, Bacteroidetes, and Verrucomicrobiota. The root endophytic Proteobacteria and Acidobacteria were significantly higher in abundance (p < 0.05) in the IMS than in the TMS, while Actinobacteria and Firmicutes were significantly lower in abundance. Five taxa were assigned to Proteobacteria and Acidobacteria, which were identified as keystones in the rhizosphere soil microbiome, while two species taxonomically affiliated with Proteobacteria were identified as keystones in the root endophytic microbiota, indicating this phylum can be an indicator for a root-associated microbiome in response to IMS. The soil pH, soil total organic carbon (TOC), total nitrogen (TN), total phosphorus (TP), available potassium (AK), and TOC:TP ratio were significantly correlated (p < 0.05) with the bacterial community composition of both rhizosphere soils and root endophytes. TMS increased the microbial network complexity of root endophytes but decreased the microbial network complexity of rhizosphere soil. Our results suggest IMS shapes the rhizosphere and endophytic bacterial community compositions and their interactions differently, which should be paid attention to when designing management practices for the sustainable development of forest ecosystems.

Microbiota Communities of Healthy and Bacterial Pustule Diseased Soybean

Soybean is an important source of protein and for a wide range of agricultural, food, and industrial applications. Soybean is being affected by Xanthomonas citri pv. glycines, a causal pathogen of bacterial pustule disease, result in a reduction in yield and quality. Diverse microbial communities of plants are involved in various plant stresses is known. Therefore, we designed to investigate the microbial community differentiation depending on the infection of X. citri pv. glycines. The microbial community's abundance, diversity, and similarity showed a difference between infected and non-infected soybean. Microbiota community analysis, excluding X. citri pv. glycines, revealed that Pseudomonas spp. would increase the population of the infected soybean. Results of DESeq analyses suggested that energy metabolism, secondary metabolite, and TCA cycle metabolism were actively diverse in the non-infected soybeans. Additionally, Streptomyces bacillaris S8, an endophyte microbiota member, was nominated as a key microbe in the healthy soybeans. Genome analysis of S. bacillaris S8 presented that salinomycin may be the critical antibacterial metabolite. Our findings on the composition of soybean microbiota communities and the key strain information will contribute to developing biological control strategies against X. citri pv. glycines.

Correlating the above- and belowground genotype of Pinus pinaster trees and rhizosphere bacterial communities under drought conditions

Increasing temperatures along with severe droughts are factors that may jeopardize the survival of the forests in the Mediterranean basin. In this region, Pinus pinaster is a common conifer species, that has been used as a model species in evolutionary studies due to its adaptive response to changing environments. Although its drought tolerance mechanisms are already known, knowledge about the dynamics of its root microbiota is still scarce. We aimed to decipher the structural (bacterial abundance), compositional, functional and associative changes of the P. pinaster rhizosphere bacterial communities in spring and summer, at DNA and RNA level (environmental DNA, live and dead cells, and those synthesizing proteins). A fundamental aspect of root microbiome-based approaches is to guarantee the correct origin of the samples. Thus, we assessed the genotype of host needles and roots from which rhizosphere samples were obtained. For more than 50% of the selected trees, genotype discrepancies were found and in three cases the plant species could not be determined. Rhizosphere bacterial communities were homogeneous with respect to diversity and structural levels regardless of the host genotype in both seasons. Nonetheless, significant changes were seen in the taxonomic profiles depending on the season. Seasonal changes were also evident in the bacterial co-occurrence patterns, both in DNA and RNA libraries. While spring communities switched to more complex networks, summer populations resulted in more compartmentalized networks, suggesting that these communities were facing a disturbance. These results may mirror the future status of bacterial communities in a context of climate change. A keystone hub was ascribed to the genus Phenylobacterium in the functional network calculated for summer. Overall, it is important to validate the origin and identity of plant samples in any plant-microbiota study so that more reliable ecological analyses are performed.

Conventional vs. Organic Agriculture-Which One Promotes Better Yields and Microbial Resilience in Rapidly Changing Climates?

In recent years, agricultural productivity has been affected dramatically by climate-related events such as drought. On the other hand, agricultural intensification is expected to increase to satisfy the need for increased global food production. Microbes associated with soil and plants produce a range of bioactive natural products that significantly contribute to crop stress tolerance. Therefore, a better understanding of the parallel effects of agricultural management (conventional and organic croplands) and climate conditions on soil-microbe-plant interactions is crucial to maximizing the effort in engineering a plant microbiome that can better support productivity in agroecosystems. This paper provides a general overview of the major current debates on conventional and organic farming performance regarding yields, particularly under ambient and future climate conditions. With the main focus on cropland, the effect of agricultural management on soil and plant microbiomes is discussed. In addition, the advantage of incorporating microbiome-based approaches into current farming practices to ensure agricultural productivity with less adverse environmental impacts is highlighted. To enhance crop production under organic farming without massive land-use changes and expansion of farmland, the microbial-based approach can be used to ensure higher productivity, particularly under a rapidly changing climate.

Biostimulant Effects of Chaetomium globosum and Minimedusa polyspora Culture Filtrates on Cichorium intybus Plant: Growth Performance and Metabolomic Traits

In this study, we investigated the biostimulant effect of fungal culture filtrates obtained from Chaetomium globosum and Minimedusa polyspora on growth performance and metabolomic traits of chicory (Cichorium intybus) plants. For the first time, we showed that M. polyspora culture filtrate exerts a direct plant growth-promoting effect through an increase of biomass, both in shoots and roots, and of the leaf area. Conversely, no significant effect on morphological traits and biomass yield was observed in C. intybus plants treated with C. globosum culture filtrate. Based on ¹H-NMR metabolomics data, differential metabolites and their related metabolic pathways were highlighted. The treatment with C. globosum and M. polyspora culture filtrates stimulated a common response in C. intybus roots involving the synthesis of 3-OH-butyrate through the decrease in the synthesis of fatty acids and sterols, as a mechanism balancing the NADPH/NADP⁺ ratio. The fungal culture filtrates differently triggered the phenylpropanoid pathway in C. intybus plants: C. globosum culture filtrate increased phenylalanine and chicoric acid in the roots, whereas M. polyspora culture filtrate stimulated an increase of 4-OH-benzoate. Chicoric acid, whose biosynthetic pathway in the chicory plant is putative and still not well known, is a very promising natural compound playing an important role in plant defense. On the contrary, benzoic acids serve as precursors for a wide variety of essential compounds playing crucial roles in plant fitness and defense response activation. To the best of our knowledge, this is the first study that shows the biostimulant effect of C. globosum and M. polyspora culture filtrates on C. intybus growth and metabolome, increasing the knowledge on fungal bioresources for the development of biostimulants.

Ecology and diversity of culturable fungal species associated with soybean seedling diseases in the Midwestern United States

AIMS

To isolate and characterize fungi associated with diseased soybean seedlings in Midwestern soybean production fields and to determine the influence of environmental and edaphic factors on their incidence.

METHODS AND RESULTS

Seedlings were collected from fields with seedling disease history in 2012 and 2013 for fungal isolation. Environmental and edaphic data associated with each field was collected. 3036 fungal isolates were obtained and assigned to 76 species. The most abundant genera recovered were Fusarium (73%) and Trichoderma (11.2%). Other genera included Mortierella, Clonostachys, Rhizoctonia, Alternaria, Mucor, Phoma, Macrophomina and Phomopsis. Most recovered species are known soybean pathogens. However, non-pathogenic organisms were also isolated. Crop history, soil density, water source, precipitation and temperature were the main factors influencing the abundance of fungal species.

CONCLUSION

Key fungal species associated with soybean seedling diseases occurring in several US production regions were characterized. This work also identified major environment and edaphic factors affecting the abundance and occurrence of these species.

SIGNIFICANCE AND IMPACT OF THE STUDY

The identification and characterization of the main pathogens associated with seedling diseases across major soybean-producing areas could help manage those pathogens, and devise more effective and sustainable practices to reduce the damage they cause.

Genomics and Informatics, Conjoined Tools Vital for Understanding and Protecting Plant Health

Genomics' impact on crop production continuously expands. The number of sequenced plant and microbial species and strains representing diverse populations of individual species rapidly increases thanks to the advent of next-generation sequencing technologies. Their genomic blueprints revealed candidate genes involved in various functions and processes crucial for crop health and helped in understanding how the sequenced organisms have evolved at the genome level. Functional genomics quickly translates these blueprints into a detailed mechanistic understanding of how such functions and processes work and are regulated; this understanding guides and empowers efforts to protect crops from diverse biotic and abiotic threats. Metagenome analyses help identify candidate microbes crucial for crop health and uncover how microbial communities associated with crop production respond to environmental conditions and cultural practices, presenting opportunities to enhance crop health by judiciously configuring microbial communities. Efficient conversion of disparate types of massive genomics data into actionable knowledge requires a robust informatics infrastructure supporting data preservation, analysis, and sharing. This review starts with an overview of how genomics came about and has quickly transformed life science. We illuminate how genomics and informatics can be applied to investigate various crop health-related problems using selected studies. We end the review by noting why community empowerment via crowdsourcing is crucial to harnessing genomics to protect global food and nutrition security without continuously expanding the environmental footprint of crop production.

A Nematode Community-Based Integrated Productivity Efficiency (IPE) Model That Identifies Sustainable Soil Health Outcomes: A Case of Compost Application in Carrot Production

Percent soil organic matter (SOM), pH and crop yield are among the biophysicochemical process-driven soil health indicators (SHIs). However, identifying sustainable soil health conditions using these SHIs is limited due to the lack of Integrated Productivity Efficiency (IPE) models. We define IPE as a concept that identifies best-to-worst-case soil health outcomes by assessing the effect of agronomic practices on weighted abundance of functional guilds (WAFG) of beneficial soil organisms and SHIs simultaneously. Expressing WAFG of all beneficial nematodes (x-axis) and SHIs (y-axis) as a percent of untreated control and regression of x and y reveals four quadrants describing worst-to-best-case outcomes for soil health and sustainability. We tested the effects of composted cow manure (AC) and plant litter (PC) applied at 135 (1×), 203 (1.5×), and 270 (2×) kg N/ha on WAFG, SOM, pH, and yield in a sandy clay loam field of a processing carrot cultivar over three growing seasons. Untreated control and urea at 1× served as experimental controls. Data that varied by time and were difficult to make sense of were separated into sustainable, unsustainable, or requiring specific modification to be sustainable categories by the IPE model. Within the sustainable category, all AC treatments and 2× rate of PC treatments had the best integrated efficiency outcomes across the SHIs. The IPE model provides a platform where other biophysicochemical process-driven SHIs could be integrated.

Soil Origin and Plant Genotype Modulate Switchgrass Aboveground Productivity and Root Microbiome Assembly

Switchgrass (Panicum virgatum) is a model perennial grass for bioenergy production that can be productive in agricultural lands that are not suitable for food production. There is growing interest in whether its associated microbiome may be adaptive in low- or no-input cultivation systems. However, the relative impact of plant genotype and soil factors on plant microbiome and biomass are a challenge to decouple. To address this, a common garden greenhouse experiment was carried out using six common switchgrass genotypes, which were each grown in four different marginal soils collected from long-term bioenergy research sites in Michigan and Wisconsin. We characterized the fungal and bacterial root communities with high-throughput amplicon sequencing of the ITS and 16S rDNA markers, and collected phenological plant traits during plant growth, as well as soil chemical traits. At harvest, we measured the total plant aerial dry biomass. Significant differences in richness and Shannon diversity across soils but not between plant genotypes were found. Generalized linear models showed an interaction between soil and genotype for fungal richness but not for bacterial richness. Community structure was also strongly shaped by soil origin and soil origin × plant genotype interactions. Overall, plant genotype effects were significant but low. Random Forest models indicate that important factors impacting switchgrass biomass included NO₃⁻, Ca²⁺, PO₄³⁻, and microbial biodiversity. We identified 54 fungal and 52 bacterial predictors of plant aerial biomass, which included several operational taxonomic units belonging to Glomeraceae and Rhizobiaceae, fungal and bacterial lineages that are involved in provisioning nutrients to plants.

The Role of Soil Microbial Diversity in the Conservation of Native Seed Bacterial Microbiomes

Research into understanding the structure, composition and vertical transmission of crop seed microbiomes has intensified, although there is much less research into the seed microbiomes of crop wild relatives. Our previous study showed that the standard seed storage procedures (e.g., seed drying and storage temperature) can influence the seed microbiome of domesticated Glycine max. In this study, we characterized the seed microbiota of Glycine clandestina, a perennial wild relative of soybean (G. max (L.) Merr.) to expand our understanding about the effect of other storage procedures such as the periodic regeneration of seed stocks to bulk up seed numbers and secure viability on the seed microbiome of said seed. The G. clandestina microbiota was analysed from Generation 1 (G1) and Generation 2 (G2) seed and from mature plant organs grown in two different soil treatments T (treatment [native soil + potting mix]) and C (control [potting mix only]). Our dataset showed that soil microbiota had a strong influence on next generation seed microbiota, with an increased contribution of root microbiota by 90% and seed transmissibility by 36.3% in G2 (T) seed. Interestingly, the G2 seed microbiota primarily consisted of an initially low abundance of taxa present in G1 seed. Overall, our results indicate that seed regeneration can affect the seed microbiome composition and using native soil from the location of the source plant can enhance the conservation of the native seed microbiota.

Non-target impacts of fungicide disturbance on phyllosphere yeasts in conventional and no-till management

Fungicides reduce fungal pathogen populations and are essential to food security. Understanding the impacts of fungicides on crop microbiomes is vital to minimizing unintended consequences while maintaining their use for plant protection. However, fungicide disturbance of plant microbiomes has received limited attention, and has not been examined in different agricultural management systems. We used amplicon sequencing of fungi and prokaryotes in maize and soybean microbiomes before and after foliar fungicide application in leaves and roots from plots under long-term no-till and conventional tillage management. We examined fungicide disturbance and resilience, which revealed consistent non-target effects and greater resiliency under no-till management. Fungicides lowered pathogen abundance in maize and soybean and decreased the abundance of Tremellomycetes yeasts, especially Bulleribasidiaceae, including core microbiome members. Fungicide application reduced network complexity in the soybean phyllosphere, which revealed altered co-occurrence patterns between yeast species of Bulleribasidiaceae, and Sphingomonas and Hymenobacter in fungicide treated plots. Results indicate that foliar fungicides lower pathogen and non-target fungal abundance and may impact prokaryotes indirectly. Treatment effects were confined to the phyllosphere and did not impact belowground microbial communities. Overall, these results demonstrate the resilience of no-till management to fungicide disturbance, a potential novel ecosystem service provided by no-till agriculture.

Soybean Roots and Soil From High- and Low-Yielding Field Sites Have Different Microbiome Composition

The occurrence of high- (H) and low- (L) yielding field sites within a farm is a commonly observed phenomenon in soybean cultivation. Site topography, soil physical and chemical attributes, and soil/root-associated microbial composition can contribute to this phenomenon. In order to better understand the microbial dynamics associated with each site type (H/L), we collected bulk soil (BS), rhizosphere soil (RS), and soybean root (R) samples from historically high and low yield sites across eight Pennsylvania farms at V1 (first trifoliate) and R8 (maturity) soybean growth stages (SGS). We extracted DNA extracted from collected samples and performed high-throughput sequencing of PCR amplicons from both the fungal ITS and prokaryotic 16S rRNA gene regions. Sequences were then grouped into amplicon sequence variants (ASVs) and subjected to network analysis. Based on both ITS and 16S rRNA gene data, a greater network size and edges were observed for all sample types from H-sites compared to L-sites at both SGS. Network analysis suggested that the number of potential microbial interactions/associations were greater in samples from H-sites compared to L-sites. Diversity analyses indicated that site-type was not a main driver of alpha and beta diversity in soybean-associated microbial communities. L-sites contained a greater percentage of fungal phytopathogens (ex: Fusarium, Macrophomina, Septoria), while H-sites contained a greater percentage of mycoparasitic (ex: Trichoderma) and entomopathogenic (ex: Metarhizium) fungal genera. Furthermore, roots from H-sites possessed a greater percentage of Bradyrhizobium and genera known to contain plant growth promoting bacteria (ex: Flavobacterium, Duganella). Overall, our results revealed that there were differences in microbial composition in soil and roots from H- and L-sites across a variety of soybean farms. Based on our findings, we hypothesize that differences in microbial composition could have a causative relationship with observed within-farm variability in soybean yield.

Application of Nematode Community Analyses-Based Models towards Identifying Sustainable Soil Health Management Outcomes: A Review of the Concepts

Soil health connotes the balance of biological, physicochemical, nutritional, structural, and water-holding components necessary to sustain plant productivity. Despite a substantial knowledge base, achieving sustainable soil health remains a goal because it is difficult to simultaneously: (i) improve soil structure, physicochemistry, water-holding capacity, and nutrient cycling; (ii) suppress pests and diseases while increasing beneficial organisms; and (iii) improve biological functioning leading to improved biomass/crop yield. The objectives of this review are (a) to identify agricultural practices (APs) driving soil health degradations and barriers to developing sustainable soil health, and (b) to describe how the nematode community analyses-based soil food web (SFW) and fertilizer use efficiency (FUE) data visualization models can be used towards developing sustainable soil health. The SFW model considers changes in beneficial nematode population dynamics relative to food and reproduction (enrichment index, EI; y-axis) and resistance to disturbance (structure index, SI; x-axis) in order to identify best-to-worst case scenarios for nutrient cycling and agroecosystem suitability of AP-driven outcomes. The FUE model visualizes associations between beneficial and plant-parasitic nematodes (x-axis) and ecosystem services (e.g., yield or nutrients, y-axis). The x-y relationship identifies best-to-worst case scenarios of the outcomes for sustainability. Both models can serve as platforms towards developing integrated and sustainable soil health management strategies on a location-specific or a one-size-fits-all basis. Future improvements for increased implementation of these models are discussed.

Effects of Soybean Cultivar, Foliar Application of Azoxystrobin, and Year on Seed Vigor and Microflora Under Delayed Harvest Conditions

The effects of cultivar and foliar fungicide applications on soybean seed germination, vigor, microflora, and yield after delayed harvest were determined at the University of Arkansas Vegetable Research Station in Kibler, AR, from 2008 to 2010. Seven cultivars with varying levels of resistance to Diaporthe spp. or Cercospora spp. were treated or not treated with a foliar application of azoxystrobin at the R5 growth stage. Plots were harvested 3 weeks after the plants had reached harvest maturity. Yields were recorded, samples of seed were collected, and standard germination (SG) and accelerated aging (AA) were assessed. Seeds were also assayed for infection by fungi on modified potato dextrose agar and by bacteria on nutrient agar. Seed vigor was significantly reduced by infection with Diaporthe spp., Fusarium spp., and Bacillus subtilis, but not with Cercospora spp. Cultivar had a significant impact on yield, seed vigor, and seed infection levels. The cultivar Osage had consistently high seed vigor and low overall seed infection incidence throughout the study. MO/PSD-0259, AG 4403, and UA 4805 also had relatively high seed vigor and low seed infection rates. PI 80837 had a low incidence of seed infection by Diaporthe spp. and Fusarium spp. in 2008 and 2010, but high levels in 2009, when environmental conditions were especially favorable for these pathogens. AP 350 and Suweon97 had relatively high seed infection incidences, particularly of Diaporthe spp. and Fusarium spp., and relatively low seed vigor. Application of the foliar fungicide azoxystrobin at the R5 growth stage significantly increased AA across years and cultivars and increased seed infection by Diaporthe spp. in 2009 across cultivars. There were significant negative correlations between yield and seed infection by Diaporthe spp. and Bacillus subtilis during 1 year and with Fusarium spp. during all 3 years. Overall, resistance to seed infection can persist even when harvest is delayed. In addition to Diaporthe spp., other seedborne pathogens may reduce seed vigor and yield.

Microbial community analysis of soils under different soybean cropping regimes in the Argentinean south-eastern Humid Pampas

Soil microbial communities are key players of ecosystem processes and important for crop and soil health. The Humid Pampas region in Argentina concentrates 75% of the national soybean production, which is based on intensive use of agrochemicals, monocropping and no-till. A long-term field experiment under no-till management in the southeast of the Argentinean Pampas provides a unique opportunity to compare soybean under monocropping with cultivation including alternating cover crops or in a three-phase rotation. We hypothesized that cropping regimes and season affect soil microbial community composition and diversity. Amplicon sequencing of 16S rRNA genes and internal transcribed spacer fragments showed a stronger microbial seasonal dynamic in conservation regimes compared to monocropping. In addition, several bacterial (e.g. Catenulispora, Streptomyces and Bacillus) and fungal genera (e.g. Exophiala) with cropping regime-dependent differential relative abundances were identified. Despite a temporal shift in microbial and chemical parameters, this study shows that long-term cropping regimes shaped the soil microbiota. This might have important implications for soil quality and soybean performance and should therefore be considered in the development of sustainable agricultural managements.