Open Access and Reproducibility in Plant Pathology Research: Guidelines and Best Practices

The landscape of scientific publishing is experiencing a transformative shift toward open access, a paradigm that mandates the availability of research outputs such as data, code, materials, and publications. Open access provides increased reproducibility and allows for reuse of these resources. This article provides guidance for best publishing practices of scientific research, data, and associated resources, including code, in The American Phytopathological Society journals. Key areas such as diagnostic assays, experimental design, data sharing, and code deposition are explored in detail. This guidance aligns with that observed by other leading journals. We hope the information assembled in this paper will raise awareness of best practices and enable greater appraisal of the true effects of biological phenomena in plant pathology.

Evaluation of Bait Crops for the Integrated Management of White Rot (Sclerotium cepivorum) in Allium Crops

White rot, caused by Sclerotium cepivorum, is a serious disease that causes significant yield losses in Allium production. The pathogen persists in soil as sclerotia, which germinate in response to sulfur compounds in Allium root exudates. This study was aimed at investigating the potential of early-terminated Allium bait crops to reduce densities of S. cepivorum sclerotia in soil. In growth chamber experiments with white onion (A. cepa cultivar 'Southport White Globe'), red onion (A. cepa cultivar 'Marenge'), sweet onion (A. cepa cultivar 'Walla Walla'), and bunching onion (A. fistulosum cultivar 'Parade'), termination of all four Alliums at the first- and second-leaf stages reduced soil sclerotia populations by up to 62 and 76%, respectively. Examination of soil samples collected 4 weeks after crop termination indicated that sclerotia populations in bait crop treatments remained low when seedlings were terminated at the first- and second-leaf stages. In contrast, crop termination at the third-leaf stage resulted in an increase in sclerotia counts due to the pathogen reproduction on the bait crops. The reduction in sclerotia populations in soil due to early crop termination was also observed in replicated field trials. Greater reductions in sclerotia counts were observed when plants in these experiments were terminated chemically as opposed to mechanically. In-furrow fungicides did not reduce sclerotia numbers under the conditions tested. This study demonstrates the potential for early termination of Allium bait crops to help reduce white rot inoculum in soil.

Legacy effects of fumigation on soil bacterial and fungal communities and their response to metam sodium application

BACKGROUND

Soil microorganisms are integral to maintaining soil health and crop productivity, but fumigation used to suppress soilborne diseases may affect soil microbiota. Currently, little is known about the legacy effects of soil fumigation on soil microbial communities and their response to fumigation at the production scale. Here, 16S rRNA gene and internal transcribed spacer amplicon sequencing was used to characterize the bacterial and fungal communities in soils from intensively managed crop fields with and without previous exposure to metam sodium (MS) fumigation. The effect of fumigation history, soil series, and rotation crop diversity on microbial community variation was estimated and the response of the soil microbiome to MS application in an open microcosm system was documented.

RESULTS

We found that previous MS fumigation reduced soil bacterial diversity but did not affect microbial richness and fungal diversity. Fumigation history, soil series, and rotation crop diversity were the main contributors to the variation in microbial β-diversity. Between fumigated and non-fumigated soils, predominant bacterial and fungal taxa were similar; however, their relative abundance varied with fumigation history. In particular, the abundance of Basidiomycete yeasts was decreased in fumigated soils. MS fumigation also altered soil bacterial and fungal co-occurrence network structure and associations. In microcosms, application of MS reduced soil microbial richness and bacterial diversity. Soil microbial β-diversity was also affected but microbial communities of the microcosm soils were always similar to that of the field soils used to establish the microcosms. MS application also induced changes in relative abundance of several predominant bacterial and fungal genera based on a soil's previous fumigation exposure.

CONCLUSIONS

The legacy effects of MS fumigation are more pronounced on soil bacterial diversity, β-diversity and networks. Repeated fumigant applications shift soil microbial compositions and may contribute to differential MS sensitivity among soil microorganisms. Following MS application, microbial richness and bacterial diversity decreases, but microbial β-diversity was similar to that of the field soils used to establish the microcosms in the short-term (< 6 weeks). The responses of soil microbiome to MS fumigation are context dependent and rely on abiotic, biotic, and agricultural management practices.

Afternoon Ascospore Release in Claviceps purpurea Optimizes Perennial Ryegrass Infection

In Kentucky bluegrass (Poa pratensis), Claviceps purpurea, the causal agent of ergot, typically releases ascospores during the early-morning hours, between about midnight and 10:00 a.m., corresponding to time of flowering, when the unfertilized ovaries are most susceptible to infection. During aeromycology studies of C. purpurea in perennial ryegrass (Lolium perenne) in northeastern Oregon during 2008 to 2010 and 2013, a strain of C. purpurea was found that released ascospores in the afternoon, coinciding with flowering in perennial ryegrass. Under controlled environmental conditions, sclerotia from perennial ryegrass and Kentucky bluegrass released spores in the afternoon and morning, respectively, consistent with timing of spore release under field conditions. Internal transcribed spacer (ITS) sequences of single sclerotial isolates from Kentucky bluegrass and perennial ryegrass were consistent with C. purpurea, although minor variations in ITS sequences among isolates were noted. Differences between Kentucky bluegrass and perennial ryegrass isolates were observed in random amplified polymorphic DNA. Evidence is provided for adaptation of C. purpurea to perennial ryegrass by means of delayed spore release that coincides with afternoon flowering in perennial ryegrass.