Integration of Phenotypes in Microbiome Networks for Designing Synthetic Communities: a Study of Mycobiomes in the Grafted Tomato System.

Understanding factors influencing microbial interactions, and designing methods to identify key taxa that are candidates for synthetic communities, or SynComs, are complex challenges for achieving microbiome-based agriculture. Here, we study how grafting and the choice of rootstock influences root-associated fungal communities in a grafted tomato system. We studied three tomato rootstocks (BHN589, RST-04-106, and Maxifort) grafted to a BHN589 scion and profiled the fungal communities in the endosphere and rhizosphere by sequencing the internal transcribed spacer (ITS2). The data provided evidence for a rootstock effect (explaining ~2% of the total captured variation, P < 0.01) on the fungal community. Moreover, the most productive rootstock, Maxifort, supported greater fungal species richness than the other rootstocks or controls. We then constructed a phenotype-operational taxonomic unit (OTU) network analysis (PhONA) using an integrated machine learning and network analysis approach based on fungal OTUs and associated tomato yield as the phenotype. PhONA provides a graphical framework to select a testable and manageable number of OTUs to support microbiome-enhanced agriculture. We identified differentially abundant OTUs specific to each rootstock in both endosphere and rhizosphere compartments. Subsequent analyses using PhONA identified OTUs that were directly associated with tomato fruit yield and others that were indirectly linked to yield through their links to these OTUs. Fungal OTUs that are directly or indirectly linked with tomato yield may represent candidates for synthetic communities to be explored in agricultural systems. IMPORTANCE The realized benefits of microbiome analyses for plant health and disease management are often limited by the lack of methods to select manageable and testable synthetic microbiomes. We evaluated the composition and diversity of root-associated fungal communities from grafted tomatoes. We then constructed a phenotype-OTU network analysis (PhONA) using these linear and network models. By incorporating yield data in the network, PhONA identified OTUs that were directly predictive of tomato yield and others that were indirectly linked to yield through their links to these OTUs. Follow-up functional studies of taxa associated with effective rootstocks, identified using approaches such as PhONA, could support the design of synthetic fungal communities for microbiome-based crop production and disease management. The PhONA framework is flexible for incorporation of other phenotypic data, and the underlying models can readily be generalized to accommodate other microbiome or 'omics data.

Rootstocks Shape the Rhizobiome: Rhizosphere and Endosphere Bacterial Communities in the Grafted Tomato System.

Root-associated microbes are critical to plant health and performance, although understanding of the factors that structure these microbial communities and the theory to predict microbial assemblages are still limited. Here, we use a grafted tomato system to study the effects of rootstock genotypes and grafting in endosphere and rhizosphere microbiomes that were evaluated by sequencing 16S rRNA. We compared the microbiomes of nongrafted tomato cultivar BHN589, self-grafted BHN589, and BHN589 grafted to Maxifort or RST-04-106 hybrid rootstocks. Operational taxonomic unit (OTU)-based bacterial diversity was greater in Maxifort compared to the nongrafted control, whereas bacterial diversity in the controls (self-grafted and nongrafted) and the other rootstock (RST-04-106) was similar. Grafting itself did not affect bacterial diversity; diversity in the self-graft was similar to that of the nongraft. Bacterial diversity was higher in the rhizosphere than in the endosphere for all treatments. However, despite the lower overall diversity, there was a greater number of differentially abundant OTUs (DAOTUs) in the endosphere, with the greatest number of DAOTUs associated with Maxifort. In a permutational multivariate analysis of variance (PERMANOVA), there was evidence for an effect of rootstock genotype on bacterial communities. The endosphere-rhizosphere compartment and study site explained a high percentage of the differences among bacterial communities. Further analyses identified OTUs responsive to rootstock genotypes in both the endosphere and rhizosphere. Our findings highlight the effects of rootstocks on bacterial diversity and composition. The influence of rootstock and plant compartment on microbial communities indicates opportunities for the development of designer communities and microbiome-based breeding to improve future crop production.IMPORTANCE Understanding factors that control microbial communities is essential for designing and supporting microbiome-based agriculture. In this study, we used a grafted tomato system to study the effect of rootstock genotypes and grafting on bacterial communities colonizing the endosphere and rhizosphere. To compare the bacterial communities in control treatments (nongrafted and self-grafted plants) with the hybrid rootstocks used by farmers, we evaluated the effect of rootstocks on overall bacterial diversity and composition. These findings indicate the potential for using plant genotype to indirectly select bacterial taxa. In addition, we identify taxa responsive to each rootstock treatment, which may represent candidate taxa useful for biocontrol and in biofertilizers.

Evidence that prohexadione-calcium induces structural resistance to fire blight infection.

Mechanisms of fire blight control by the shoot-growth regulator prohexadione-calcium (ProCa) were investigated by comparing disease development in ProCa-treated potted apple trees (cv. Gala) to paclobutrazol (another shoot-growth regulator)-treated and nontreated trees and in ProCa-treated cv. McIntosh trees in the field. Twenty-eight days after inoculation with Erwinia amylovora Ea110, disease incidence on ProCa- and paclobutrazol-treated shoots was significantly reduced compared with that on nontreated shoots. Disease severity (percent shoot length infected) was also significantly lower on both ProCa- and paclobutrazol-treated shoots than on nontreated shoots. However, bacterial populations within inoculated shoots were high and bacterial growth occurred in all treatments. In addition, the mean cell wall width of the cortical parenchyma midvein tissue of the first and second youngest unfolded leaves of ProCa- and paclobutrazol-treated shoots was significantly wider both 0.5 and 2 cm from the leaf tips compared with the cell walls of the nontreated tissue. Taken together, these results suggest that reduction of fire blight symptoms by ProCa and paclobutrazol is not the result of reduced populations of E. amylovora in shoots. Moreover, because paclobutrazol also reduced disease severity and incidence, changes in flavonoid metabolism induced by ProCa but not paclobutrazol does not appear to be responsible for disease control as suggested in recent literature. Finally, although this study did not directly link disease control to the observed cell wall changes, the possibility that an increase in cell wall width impedes the spread of E. amylovora should be investigated in more depth.

Vapor Activity and Systemic Movement of Mefenoxam Control Grapevine Downy Mildew.

Metalaxyl is translocated from roots to leaves to control a number of oomycete pathogens, but systemic movement from vegetative organs into fruit and vapor activity against Plasmopara viticola, the causal agent of grapevine downy mildew, has not been examined experimentally. We inoculated fruit clusters of grapevines with P. viticola at prebloom, bloom, or 1 week postbloom. We then selectively applied mefenoxam (288 mg/liter), the active enantiomer of metalaxyl, to the leaves or stem tissue 12 to 48 h after inoculation. Little to no downy mildew developed on fruit when mefenoxam was applied to leaf tissue, stem tissue, or both. In contrast, downy mildew symptoms were severe on inoculated clusters on untreated shoots. When potential vapor activity was blocked, we observed fungicidal activity on seedling foliage in response to apparent systemic movement from treated stems and soil, but not from leaves. However, when vapor activity was permitted, mefenoxam residues on treated leaves controlled disease on other, untreated leaves. In subsequent vineyard experiments, vapor and systemic activity provided equivalent and near-complete suppression of downy mildew on clusters 48 h post inoculation. Furthermore, inoculated grape seedlings that were placed near mefenoxam-treated seedlings in open and closed systems developed nil to trace levels of downy mildew compared with controls, further indicating that the material has strong vapor activity.

Primary Infection, Lesion Productivity, and Survival of Sporangia in the Grapevine Downy Mildew Pathogen Plasmopara viticola.

ABSTRACT Several aspects of grapevine downy mildew epidemiology that are fundamental to model predictions were investigated. Simple rainfall-, temperature-, and phenology-based thresholds (rain > 2.5 mm; temperature > 11 degrees C; and phenology > Eichorn and Lorenz [E&L] growth stage 12) were evaluated to forecast primary (oosporic) infection by Plasmopara viticola. The threshold was consistent across 15 years of historical data on the highly susceptible cv. Chancellor at one site, and successfully predicted the initial outbreak of downy mildew for 2 of 3 years at three additional sites. Field inoculations demonstrated that shoot tissue was susceptible to infection as early as E&L stage 5, suggesting that initial germination of oospores, rather than acquisition of host susceptibility, was probably the limiting factor in the initiation of disease outbreaks. We also found that oospores may continue to germinate and cause infections throughout the growing season, in contrast to the widely-held assumption that the supply of oospores is depleted shortly after bloom. Lesion productivity (sporangia/lesion) did not decline with age of a lesion in the absence of suitable weather to induce sporulation. However, the productivity of all lesions declined rapidly through repeated cycles of sporulation. Extremely high temperatures (i.e., one day reaching 42.8 degrees C) had an eradicative effect under vineyard conditions, and permanently reduced sporulation from existing (but not incubating) lesions to trace levels, despite a later return to weather conducive to sporulation. In fair weather, most sporangia died sometime during the daylight period immediately following their production. However, over 50% of sporangia still released zoospores after 12 to 24 h of exposure to overcast conditions.

Seasonal development of ontogenic resistance to downy mildew in grape berries and rachises.

ABSTRACT Clusters of Vitis vinifera and V. labrusca are reported to become resistant to Plasmopara viticola at stages of development ranging from 1 to 6 weeks postbloom. It has been suggested that resistance is associated with loss of the infection court as stomata are converted to lenticels, but the time of onset, cultivar variation, and seasonal variation in ontogenic resistance has remained uncertain, as has the comparative susceptibility of stem tissue within the fruit cluster. In New York, we inoculated clusters of V. vinifera cvs. Chardonnay and Riesling and V. labrusca cvs. Concord and Niagara at stages from prebloom until 5 to 6 weeks postbloom. Berries were infected and supported profuse sporulation until 2 weeks postbloom, and pedicel tissue remained susceptible until 4 weeks postbloom. Although berries on later-inoculated clusters failed to support sporulation, discoloration and necrosis of berry tissues was often noted, and necrosis of the pedicel within such clusters often led to further discoloration, shriveling, reduced size, or loss of berries. When the epidermis of discolored berries that initially failed to support sporulation was cut, the pathogen emerged and sporulated through incisions, indicating that lack of sporulation on older symptomatic berries was due to infection at an early stage of berry development followed by conversion of functional stomata to lenticels during latency. We repeated the study on Chardonnay and Riesling vines in South Australia and found that the period of berry and rachis susceptibility was greatly increased. The protracted susceptibility of the host was related to the increased duration and phenological heterogeneity of bloom and berry development in the warmer climate of South Australia. The time of onset and subsequent expression of ontogenic resistance to P. viticola may thus be modified by climate and should be weighed in transposing results from one climatic area to another. Our results can be used to refine forecast models for grapevine downy mildew to account for changes in berry and rachis susceptibility, and to focus fungicide application schedules upon the most critical periods for protection of fruit.