Due to the intimate association between plants and their microbial symbionts, an examination of the influence of agricultural practices on phytobiome structure and diversity could foster a more comprehensive understanding of plant health and produce safety. Indeed, the impact of upstream crop producti006Fn practices cannot be overstated in their role in assuring an abundant and safe food supply. To assess whether fertilizer type impacted rhizosphere and phyllosphere bacterial communities associating with tomato plants, the bacterial microbiome of tomato cv. 'BHN602' grown in soils amended with fresh poultry litter, commercially available sterilized poultry litter pellets, vermicompost or synthetic fertilizer was described. Culture independent DNA was extracted from bulk and rhizosphere soils, and washes of tomato blossoms and ripe fruit. PCR amplicons of hypervariable regions of the 16S rRNA gene were sequenced and profiled using the QIIME pipeline. Bulk and rhizosphere soil, and blossom and fruit surfaces all supported distinct bacterial communities according to principal coordinate analysis and ANOSIM (R=0.87, p=0.001 in year 1; R=0.93, p=0.001 in year 2). Use of microbiologically diverse organic fertilizers generally did not influence bacterial diversity, community structure or relative abundance of specific taxa on any plant organ surface. However, statistically significant differences in sand and silt contents of soil (p<0.05) across the field and corresponding shifts in water activity were positively (R=0.52, p=0.005) and negatively (R=0.48, p=0.009) correlated with changes in bacterial community structure in the rhizosphere, respectively. Over two harvest seasons, this study demonstrated that the application of raw poultry manure, poultry litter pellets and vermicompost had little effect on the tomato microbiome in the rhizosphere and phyllosphere, when compared to synthetically fertilized plants. Plant anatomy, and other factors related to field location, possibly associated with edaphic and air characteristics, were more influential drivers of different tomato organ microbiomes than were diverse soil amendment applications.

Xylosandrus germanus (Blandford) has caused increasing damage in high-density New York apple orchards since 2013, resulting in tree decline and death. We documented their occurrence and timing in > 50 orchards using ethanol-baited traps from 2014 to 2016. First captures ranged from 48 to 83 degree days (base 10 °C) from 1 January. Captures were numerically higher at the orchard-woods interface than within the orchard interior, but differences were not significant in locations with lower populations. Control using insecticide trunk sprays was tested in potted, waterlogged apple trees placed in orchards and nurseries, and inside wooded areas adjacent to orchards. A verbenone repellent was used in combination with trunk sprays to improve control. Overall, insecticide sprays were inconsistent and marginal in preventing new infestations. Chlorpyrifos significantly reduced infestations versus lambda-cyhalothrin and untreated trees at one location in the 2015 orchard trials, and versus untreated trees at one location in the 2016 nursery trials, but otherwise performed no better than other treatments. The addition of verbenone to either the check or permethrin treatments resulted in significantly fewer attack sites containing brood at one orchard site in 2016. Chlorpyrifos, lambda-cyhalothrin, and permethrin significantly reduced the number of attack sites containing adults compared with untreated trees at one nursery trial location in 2016, but were otherwise ineffective in reducing numbers of trees in other locations and infestation categories. We found several fungal and bacterial species associated with X. germanus and its infestation of apples. These microbes likely play a minimal role in apple decline.

The distribution and diversity of grapevine red blotch virus (GRBV) and wild Vitis virus 1 (WVV1) (genus Grablovirus; family Geminiviridae) were determined in free-living Vitis spp. in northern California and New York from 2013 to 2017. Grabloviruses were detected by polymerase chain reaction in 28% (57 of 203) of samples from California but in none of the 163 samples from New York. The incidence of GRBV in free-living vines was significantly higher in samples from California counties with high compared with low grape production (χ = 83.09; P < 0.001), and in samples near (<5 km) to compared with far (>5 km) from vineyards (χ = 57.58; P < 0.001). These results suggested a directional spread of GRBV inoculum predominantly from vineyards to free-living Vitis spp. WVV1 incidence was also significantly higher in areas with higher grape production acreage (χ = 16.02; P < 0.001). However, in contrast to GRBV, no differential distribution of WVV1 incidence was observed with regard to distance from vineyards (χ = 0.88; P = 0.3513). Two distinct phylogenetic clades were identified for both GRBV and WVV1 isolates from free-living Vitis spp., although the nucleotide sequence variability of the genomic diversity fragment was higher for WWV1 (94.3 to 99.8% sequence identity within clade 1 isolates and 90.1 to 100% within clade 2 isolates) than GRBV (98.3% between clade 1 isolates and 96.9 to 100% within clade 2 isolates). Additionally, evidence for intraspecific recombination events was found in WVV1 isolates and confirmed in GRBV isolates. The prevalence of grabloviruses in California free-living vines highlights the need for vigilance regarding potential grablovirus inoculum sources in order to protect new vineyard plantings and foundation stock vineyards in California.

There are still unknown factors at play in the causation of bitter pit in ‘Honeycrisp’ as well as in other apple varieties. To investigate some of these factors, we conducted a survey of 34 ‘Honeycrisp’ orchard blocks distributed across two disparate production regions in eastern New York State, representing a variety of rootstocks, over three growing seasons. Weather, soil, horticultural traits, fruit quality traits, pick timing, leaf and peel minerals were evaluated for their impact on bitter pit (BP) incidence; factors were further evaluated for their interaction with region and rootstock. ‘Honeycrisp’ trees on B.9 rootstock were smaller but with comparable terminal shoot growth when compared to those on M.26 and M.9 rootstocks. B.9 fruits, which had similar fruit size to M.26 and M.9 and had good fruit quality at harvest and after storage, were much less likely to express bitter pit symptoms compared to M.9 and M.26 rootstocks. Not all traits evaluated individually correlated significatively with bitter pit incidence after a period in storage. Depending on rootstock and region, the correlation could be significant in one situation, with no correlation at all in another. In this study, peel Mg/Ca ratio and peel Ca correlated with BP for all three rootstocks, with the strongest correlations associated with the M.9 clones. These same traits correlated with BP for both regions. Pick timing had a significant influence on BP incidence following storage, with later picks offering better bitter pit storage performance. While excessively large fruits, those in the 48 and 56 count size categories, were found to be highly susceptible to BP regardless of rootstock, B.9 BP fruit susceptibility for smaller sizes was found to be size neutral. A PLSR prediction model for each rootstock and each region showed that different variables correlated to BP depending on the situation. Thus, the results could suggest that in addition to the variables considered in this study, there are other less studied factors that can influence the expression of BP symptoms. We strongly suggest that rootstock BP performance be considered a critical parameter when planning a commercial ‘Honeycrisp’ orchard and be evaluated in rootstock breeding and development programs prior to wide commercial release.