Accurate and time- or cost-efficient methods of diagnosing infected plants are important elements of a disease management program, both with respect to roguing to reduce pathogen spread , and the efficacy of pruning to clear plants of infection . Accurate diagnosis of PD in grapevines is complicated by quantitative and qualitative differences in symptoms among cultivars and other aspects of plant condition . Our results suggest that a well-trained observer can accurately diagnose PD based on visual symptoms, particularly for advanced cases of the disease. The small number of false positives in disease category 1 and 2 vines may have been due to misdiagnosis of other biotic or abiotic factors . Alternatively, false positives might indicate bacterial populations that are near the detection limit; conventional PCR has at least as low a detection threshold as other methods that rely on the presence of live bacterial cells . Regardless, although scouting based on visual symptoms clearly captured most cases of PD in the current study,hydroponic dutch buckets some caution should be used when trying to diagnose early disease stages to ensure that vines are not needlessly removed. There is no cure for grapevines once infected with X. fastidiosa, except for recovery that can occur in some overwintering vines .
The virulent nature of X. fastidiosa in grapevines, and the corresponding high mortality rate for early season infections, increases the potential value of any cultural practices that can cure vines of infection. Moreover, new vines replanted into established vineyards generally take longer to develop compared to vines planted in newly developed vineyards, potentially due to vine-to-vine competition for resources that limits growth of replacement vines. As a result, vines replanted in mature vineyards may never reach full productivity . Thus, management practices that speed the regeneration of healthy, fully developed, and productive vines may reduce the economic loss caused by PD . A multinomial logistic regression showed significant differences in the relative frequency of different grapevine growth outcomes between the two restoration methods . Chip-budded vines showed significantly lower frequency of strong growth and significantly higher frequencies of vines with developing growth and, especially, of no growth . Nearly 30% of chip-budded vines showed no growth in the following season, compared to 0% of vines on which established shoots were trained. These results indicate that training newly produced shoots from the remaining section of the scion was more likely to result in positive regrowth outcomes. As a result, of the two methods we evaluated, training of shoots that emerge from the scion of a severely pruned trunk is recommended for restoring growth.
However, it is important to note that the current study did not estimate the amount of time required for severely pruned vines to return to full productivity. Moreover, the study did not include mature vines, in which growth responses may differ from young vines. Additional studies may be needed to quantify vine yield, and perhaps fruit quality, in severely pruned vines over multiple seasons.The usefulness of pruning for disease management depends on its ability to clear plants of pathogen infection . A comparison of symptom prevalence among severely pruned and control vines from different disease severity categories showed significant effects of the number of years after pruning , pruning treatment , and initial disease symptom category . The analysis also showed significant interactions between year and treatment and between treatment and symptom category , a non-significant interaction between year and symptom category , and a marginally significant three-way interaction . Overall, more vines had symptoms in the second year compared to the first , and there was a higher prevalence of returning symptom in vines from higher initial disease categories . Severe pruning showed an apparent benefit to reducing symptoms of PD after the first year, but this effect weakened substantially by the second year, with no differences for category 1 or 3 vines, and a slightly lower disease prevalence for severely pruned category 2 vines .
A survival analysis of severely pruned category 3 vines showed a significant difference in the rate of symptom return among plots . All vines in plots 1 to 3 had symptoms by autumn 2000, two years after pruning . In plots 4 and 5, more than 80% of vines showed symptoms after three years. Only plot 6 showed markedly lower disease prevalence; in plot 6, ~70% and 50% of severely pruned category 3 vines showed no symptoms after two and four years, respectively, versus ~36% of control vines overall, after two years. It is important to note that at the time of this study, disease pressure may not fully explain the return of symptoms in severely pruned vines. Surveys conducted during the first two years of the study throughout the entirety of the six research blocks showed that the prevalence of PD in control vines actually declined slightly from the first to the second year , but not due to an increase in replanting efforts or vine death , Rather, this decline in prevalence likely reflects overwinter recovery of mild cases of the disease . Thus, the observed return of symptoms in most severely pruned vines does not appear to be explained by reinfection with X. fastidiosa after clearing of infection during the severe-pruning process. Our results indicate that the apparent effectiveness of severe pruning depended on the initial disease severity, and the effectiveness weakened over time. This suggests at least two constraints exist regarding the general utility of pruning as a PD management tool. First, severe pruning does not appear to be useful for mild cases of PD, as many of those same vines would recover from the infection over the winter . Second, there appears to be little value in pruning severely diseased vines; the high frequency of symptom return within a few years indicates that even severe pruning does not clear most vines of X. fastidiosa infection. That leaves a statistically significant window with respect to intermediate severity cases, which may benefit from severe pruning. The apparent benefit for this category of diseased vines would stem from infections that are not so localized that they are highly susceptible to natural recovery over the winter, but also not fully systemic such that the infection has developed below the pruning point . Reliable identification of this narrow class of diseased vines may require substantial experience with PD scouting, detailed record keeping, and an appreciation for variability in symptoms or infection dynamics based on grapevine cultivar and environmental conditions . Research in other bacterial plant pathosystems has evaluated the potential benefit of pruning and whether pruning extent is related to its effectiveness at clearing hosts of infection . A study of the citrus disease huanglongbing, associated with infection by Candidatus Liberibacter spp.,bato bucket evaluated two levels of pruning severity, neither of which showed promise as a disease management tool . In this pathosystem, it is plausible that a very protracted incubation period may undermine the effectiveness of pruning, because by the time the first symptoms are visible, the infection may have already moved throughout much of the tree. Collectively, our results are more similar to a study of citrus variegated chlorosis . In this study, the presence of X. fastidiosa in plant tissues at different distances from symptomatic leaves was determined for varying levels of disease severity. X. fastidiosa was more widely distributed in trees with severe disease symptoms compared to those with early stage foliar symptoms. Although ColettaFilho et al. did not test whether pruning at various distances proximal to symptomatic leaves would eliminate X. fastidiosa infections, the current recommendation is to prune citrus material if early symptoms are present, and to not prune plants with severe disease symptoms . Citrus plant age is also an important consideration; Coletta-Filho and de Souza recommend that symptomatic citrus trees up to three-years-old be removed rather than pruned, whereas trees four-years-old or older should be pruned.
We did not examine vine age as a factor in this study, but the biology of citrus and grape differ in terms of the overwinter recovery that can occur in grape and the apparently slower movement of X. fastidiosa in citrus compared to grape. Anecdotally, the two most mature plots in our study showed the most rapid return of disease, and the youngest plot showed the slowest return. More studies of the effect of vine age are needed before concluding that interactive effects of plant age and pruning differ between the PD and citrus variegated chlorosis pathosystems.The plant microbiota, defined here as the community of bacteria, fungi, archaea, viruses, and other microscopic organisms that live on or in plant tissues , confer many services as well as disservices to their hosts, including disease development and defense , protection against herbivory , tolerance of abiotic stress , and aid in nutrient uptake . These microbial communities associate with all plant tissues , including seeds . Seeds play a major role in plant communities as agents of dispersal, genetic diversity, and regeneration , and they have significant economic and social value through agriculture . Seeds also are a major bottleneck in natural plant populations, as they face heightened mortality from abiotic stressors, pests, pathogens, and predators . As the initial source of inoculum in a plant’s life cycle, seed microbes are can be transmitted across plant generations and have lifelong impacts . Consequently, understanding how seeds acquire and interact with their microbiota, for example, via priority effects or according to the Primary Symbiont Hypothesis , has implications for improving seed health, seedling establishment, and plant community structure. Previous work on seed microbiota has primarily taken a pattern-based approach to studying assembly processes . Such an approach uses culturing and/or next-generation sequencing to compare, contrast, and correlate patterns in microbial community composition, diversity, and species co-occurrences. Typically, however, these community data provide limited insights into processes such as dispersal, microbe-plant interactions, and microbemicrobe interactions.
Given that seed microbial communities are highly variable across individual plants, plant species, and locations , such pattern-based data cannot always be used to predict assembly outcomes. Moreover, such studies often consider how these assembly processes occur at a single spatial scale . We hypothesize that a mechanistic, multi-scale approach would provide a more complete understanding of how microbial communities assemble in seeds, with the field of meta community ecology providing a theoretical framework for such an approach. Meta community theory accounts for the interaction between ecological processes and habitat heterogeneity across spatiotemporal scales to impact community patterns . This emphasis on multiple scales and heterogeneity can help explain the main drivers of community assembly and patterns of biodiversity and co-occurrence . Plant-associated microbial communities vary widely across environmental gradients and host genetics from the levels of tissues to populations . As such, treating individual plants as heterogeneous habitats for microorganisms that are embedded in a larger, heterogeneous landscape of multiple plants representing different species provides a new approach to observing, testing, and modeling drivers of microbial community variation . However, the study of microbiota through a meta community lens is still relatively new, both for animals and plants , and the plant seed represents a relatively understudied microbiome in this context. In this review, we address how mechanisms of seed microbial community assembly have been studied at different spatial micro-, meso-, and macro-scales , and advocate for a meta community-based approach to seed microbiology in future work. For this review, we use the definition of community assembly from Fukami : “the construction and maintenance of local communities through sequential, repeated immigration of species from the regional species pool.” Additionally, most studies that we cover in our review will be focused on fungi and bacteria . We acknowledge that archaea, viruses, and protists are frequent members of plant-associated microbial communities , many plant viruses are seed transmitted , and viruses can play a major role in the diversity and function of soil microbial communities . However, the ecological roles of these microbes in plant microbial communities, including those of seeds, are still largely unknown. As such, we cannot speak on their contributions to seed microbiota assembly here and recommend new research on these microbes in seeds. We will first summarize the modes of microbial acquisition into seeds, and how meta community ecology frames this assembly process. We then discuss studies of seed microbiome assembly which examine the processes of filtering, species interactions, dispersal, and ecological drift.