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This study endeavored to test two hypotheses: (i) Hyalorbilia oviparasitica and related species (H. oviparasitica clade) will be detected in sugar beet fields in California’s Imperial Valley and (ii) the population densities of these fungi will increase in the presence of their nematode host (Heterodera schachtii) and a host plant of this nematode. The H. oviparasitica clade includes potent hyperparasites of sedentary stages of plant-parasitic nematodes, which have the ability to substantially suppress the population densities of several endoparasitic nematode species. In this study, 21 of 25 Imperial Valley soils cropped to sugar beets harbored members of the H. oviparasitica clade. The population densities of these fungi increased, on average, approximately 10,000-fold in the presence of H. schachtii and its host Swiss Chard over one nematode generation. An rRNA ITS sequence analysis showed that members of the H. oviparasitica clade were the dominant group of fungi associated with H. schachtii females derived from these soils. These results provide evidence supporting the hypotheses. [Formula: see text] Copyright © 2021 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license .

Nematophagous fungi, mostly belonging to the phylum Ascomycota, have raised great attention because of their potential use against plant-pathogenic nematodes. In this investigation, entomopathogenic fungi were collected in Taiwan and isolated and identified based on molecular phylogenetic analyses of six nuclear loci including LSU, ITS, TEF1, RPB1, RPB2, and TUB2 combined with morphological data. Two novel fungal taxa are described in the present study, namely, Paraboeremia taiwanensis (Pleosporales) and Polycephalomyces elaphomyceticola (Hypocreales), respectively. Both species showed the ability to parasitize eggs of the rice root-knot nematode, Meloidogyne graminicola, in in vitro assays. Size ranges of conidiomata and conidia distinguish Paraboeremia taiwanensis from other currently known Paraboeremia species. Polycephalomyces elaphomyceticola differs from other Polycephalomyces species by producing single stromata, smaller perithecia, awl-shaped phialides, and monomorphic conidia. It was encountered as a parasite on Elaphomyces muricatus. Both examined strains grew and sporulated well on artificial media. Pathogenicity testing showed that they were capable of parasitizing eggs of Meloidogyne graminicola. In addition, our study elucidated the teleomorph of Polycephalomyces agaricus for the first time.

Plant disease and pests are the third largest source of the loss rate of crops worldwide after the loss causing by natural disaster and transportation process. Plant-parasitic nematodes (PPN) are one of the main plant pests and cause over 100 million US dollars of agricultural loss worldwide every year. In general, identifying species of nematodes from their morphological characters is the first step for a nematologist. However, limited professionals cannot fulfill the huge demand. A fast identification system for nematodes applying imaging classification methods would be a potential solution to amend the practical needs. In recent years, the rise of deep learning brought a significant breakthrough in object detection. In this study, deep learning algorithms were applied to develop the plant-parasitic nematode (PPN) image identification system. The experimental dataset included four genera (e.g., Aphelenchoides, Bursaphelenchus, Meloidogyne, and Pratylenchus) and 10 species of common PPNs worldwide. In addition, one free-living nematodes, Caenorhabditis elegans, and two entomopathogenic nematodes, Heterocephalobellus sp. and Metarhabditis amsactae, were also collected as the control group for the recognition of the non-plant-parasitic nematodes. In total, 9483 images of nematode images were acquired. Faster Region-based Convolutional Neural Network (Faster RCNN) architecture was selected to develop the PPN identification model. As a result, the model with the ResNet-101 structure achieved the highest mean average precision (mAP) of 0.9018.

Including pest resistance elements against the major local concern is naturally important in the breeding process. Oat (Avena sativa L.) has been recently reintroduced into Taiwan as a winter alternative forage crop, and its agronomic performance has been evaluated at different locations in the country. This study examined the resistance to root-knot nematode, Meloidogyne graminicola, in four oat (Avena sativa L.) breeding lines of mass planting potential for winter in Taiwan. The host attraction level to the nematode, and the penetration and reproduction ability of nematode towards host roots were evaluated by chemotaxis assay, root staining assay, root galling, and nematode extraction. Based on the gall index (GI) and multiplication factor (R), the resistance of each oat line was evaluated. At 24 h postinoculation, second-stage juvenile (J2) nematodes appeared most attracted by oat breeding lines UFRGS136104-3 and UFRGS136119-2. The number of J2s successfully penetrated into the two breeding lines were also high. However, at 40 days postinoculation, observation of the oats in the newly developed culture bag nematode-inoculation system revealed that the amount of root galls and 2nd generation nematodes were significantly higher in line LA08085BS-T2 than in other lines. In sum, oat breeding line UFRGS136104-3 was highly resistant to M. graminicola by inhibiting the gall formation and nematode reproduction, while UFRGS136106-3 and UFRGS136119-2 showed relatively weak resistance and oat line LA08085BS-T2 would be a moderately susceptible host to M. graminicola, with high numbers of root gall formation. The outcome of this study provides ground information for nematode-resistant oat cultivar breeding.

Meloidogyne enterolobii, an aggressive plant-parasitic nematode, has been causing great yield loss worldwide in recent years. With no resistant Chinese cabbage cultivar available currently, a biological control strategy is needed to offer an eco-friendly option for sustainable farming. In this study, the nematode suppression efficacy of two newly isolated fungi, Paraboeremia taiwanensis and Samsoniella sp., were evaluated against M. enterolobii and compared to the known biological control agents Hyalorbilia oviparasitica strain DoUCR50 and Purpureocillium lilacinum strain 251 (PL251). Both P. taiwanensis and Samsoniella sp. reduced 29%&ndash, 63% disease severity as effectively as the commercial product PL251 on Chinese cabbage in greenhouse trails. The in vitro egg infection rate was 47.83% by P. taiwanensis and 47.50% for Samsoniella sp., respectively. A special protocol for scanning electron microscope observation of the fungi-infected nematodes was established in this study, and the egg parasitism of the four fungi against M. enterolobii was further confirmed. For all fungi examined in this study, fungal hyphae were seen apparently penetrating into M. enterolobii eggs without destructive damage of the overall outer eggshell and the hyphae continued to grow within eggs after 6 days of infection. The results of this study imply a similar egg-parasitism mechanism for P. taiwanensis, Samsoniella sp., H. oviparasitica DoUCR50, and P. lilacinum PL251. It further enlightens the application potential of nematophagous fungi as biocontrol agents against plant-parasitic nematodes in vegetable crop management.

As the most abundant animals on earth, nematodes are a dominant component of the soil community. They play critical roles in regulating biogeochemical cycles and vegetation dynamics within and across landscapes and are an indicator of soil biological activity. Here, we present a comprehensive global dataset of soil nematode abundance and functional group composition. This dataset includes 6,825 georeferenced soil samples from all continents and biomes. For geospatial mapping purposes these samples are aggregated into 1,933 unique 1-km pixels, each of which is linked to 73 global environmental covariate data layers. Altogether, this dataset can help to gain insight into the spatial distribution patterns of soil nematode abundance and community composition, and the environmental drivers shaping these patterns., This research was supported by a grant from DOB Ecology to T.W.C., a grant from the Netherlands Organization for Scientific Research (grant 016.Veni.181.078) to S.G., grants from NSF (OPP 1115245, 1341736, 0840979) to B.J.A., by a Ramon y Cajal fellow award (RYC-2016-19939) to R.C.H., a grant from UNEP & Global Environment Facility to J.E.C., grants from NERC’s Soil Security Programme to R.D.B. (NE/M017028/1) T.C. (NE/M017036/1), a grant from FAPEMIG/FAPESP/VALE S.A.(CRA-RDP-00136-10) to L.B.C., through the strategic programme UID/BIA/04050/2013 (POCI-01-0145-FEDER-007569) awarded to S.R.C., a grant from CNPq PROTAX (562346/2010-4) to J.M.d.C.C., a grant from DFG (CRC990) to V.K. and S.S., a grant from the MSHE of Russia (AAAA-A17-117112850234-5) to A.A.K., grants from the Chinese Academy of Sciences (XDB15010402) and the National Natural Science Foundation of China (41877047) to Q.L., grants from the National Natural Science Foundation of China (31330011, 31170484) to W.L., grants from NERC (NE/ M017036/1) to M.M., grants from the Spanish Ministry of Innovation (CGL2009-14686-C02-01/02, CGL2013- 43675-P) to J.A.R.M., grant from the Spanish Ministry of Innovation (RYC-2016-19939) to R.C.H., grants from NSF (DEB-0450537, DEB-1145440) to P.M., T.O.P. and K. Powers, grants from the German Academic Exchange Service (PKZ 91540366) and NAFOSTED (106.05–2017.330) to T.A.D.N., by an ARC Discovery project (DP150104199) to U.N.N., by the National Key Research and Development Program of China (2016YFC0502101) and the National Natural Science Foundation of China (31370632) to K. Pan, a ERC Research Council Advanced grant (ERC-Adv 323020 SPECIALS) to W.H.v.d.P, a grant from the Natural Environment Research Council (NERC) to D.G.W., a grant from BAPHIQ (106AS-9.5.1-BQ-B3) to J.-i.Y., a grant from the Russian Foundation for Basic Research (18-29-05076) to A.V.T. The James Hutton Institute receives financial support from the Scottish Government Rural and Environment Science and Analytical Services (RESAS) division. Investigations in Northwest Russia were carried out under state order for IB KarRC RAS and are partially supported by the Russian Foundation for Basic Research (18-34-00849).

Microbial community structure and composition in the plant vascular endosphere has not been studied extensively especially in the context of vascular diseases. Pierce’s disease (PD) of grapevine is caused by Xylella fastidiosa, a xylem-limited bacterium. In PD-impacted vineyards, there are observations of vines that remain asymptomatic despite being under high disease pressure. Because these vines are clonal, we hypothesized that the microbial community inhabiting the grapevine vascular endosphere is a major contributor to the disease escape phenotype. We used a next-generation sequencing Illumina MiSeq-based platform to characterize the bacterial and fungal microbiome residing in the cane endosphere of grapevine that displayed severely symptomatic, to mildly symptomatic or asymptomatic disease phenotypes. Our results provide evidence that the endophytic grapevine microbial community is composed primarily of Proteobacteria and Ascomycota with Pseudomonodales and Pleosporales as the main bacterial and fungal orders, respectively. Endophytic Pseudomonas fluorescens and Achromobacter xylosoxidans showed significant negative correlations with X. fastidiosa titer. Our data suggest that the clustering of bacterial communities appeared to be driven by the abundance of both P. fluorescens and X. fastidiosa. P. fluorescens emerged as a potential driver of the disease-escape phenotype and a promising biological control agent of PD.

Introduction: Lung cancer is the leading cause of cancer-related deaths in the US. While smoking remains the most common cause for non-small cell lung cancer (NSCLC), less research exists on the role of adverse social conditions and neighborhood socioeconomic status (nSES) in the development of specific NSCLC somatic mutations. Neighborhood conditions can be influenced by economic, housing, education, transportation, and environmental factors. Understanding the relationship between NSCLC biology and nSES is vital in addressing disproportionately high rates of NSCLC incidence and poor outcomes among marginalized communities in the US. While neighborhood deprivation indices have been linked to aggressive biology in other cancers, the link to somatic mutations in NSCLC is unknown. The purpose of this analysis is to identify relationships between exposure to adverse nSES conditions and somatic KRAS mutations, a marker of aggressive NSCLC biology. Methods: We analyzed NSCLC patients who received care at the City of Hope Comprehensive Cancer Center in Duarte, CA from 2015-2018 and received somatic KRAS testing of their lung tumor tissue as a part of their care. The patients' medical record was abstracted for data including demographics and disease characteristics. The patients' home address was geocoded and assigned a census tract-level exposure to several indices of nSES conditions including the California Health Places Index (HPI), the US Department of Housing and Urban Development Labor Market Engagement Index (LME), and the Area Deprivation Index (ADI). We used several logistic regressions to model the presence of somatic KRAS mutations in relation to exposure to various adverse nSES conditions. Odds ratios (ORs) were adjusted for age at diagnosis, sex, cigarette smoking, race/ethnicity, insurance status, cancer stage, cancer histology, and exposure to PM2.5. Results: Of 426 eligible NSCLC patients, 28% tested positive for a KRAS mutation, 54% were non-Hispanic White, 66% were stage IV, and 83% had adenocarcinomas. The risk of a KRAS mutation was significantly elevated among patients living in places with lower HPI scores (OR 1.92, 95% CI: 1.11 - 3.32) and lower LME (OR 1.16, 95% CI: 1.05 - 1.28). In adjusted models, PM2.5, ADI, and other nSES indices were not significantly associated with risk of a KRAS mutation. Conclusions: We found that NSCLC patients living in deprived neighborhood conditions as measured by the California HPI and LME were more likely to have a somatic KRAS mutation. This relationship shows that nSES may be an important determinant of aggressive NSCLC biology. However, our results also indicate that deprivation is a complex mixture of domains and regionally specific influences. These findings indicate that future research may need to consider locally specific nSES measures as a dynamic marker of neighborhood conditions in addition to nationally derived indexes such as the ADI. Citation Format: Sam Wing, Ernesto Sosa, Tarik Benmarhnia, Jiue-An Yang, Stacy Gray, Marta Jankowska, Loretta Erhunmwunsee. Association of neighborhood socioeconomic status and aggressive non-small cell lung cancer biology [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2021; 2021 Apr 10-15 and May 17-21. Philadelphia (PA): AACR; Cancer Res 2021;81(13_Suppl):Abstract nr 784.

Disease resistance is one of the most successful strategies in crop protection. For example, the implementation of PI 88788 type resistance, which contains high copy numbers of Resistance to Heterodera glycines 1 (rhg1) loci, into the commercial soybean varieties of the United States has significantly reduced the yield losses caused by soybean cyst nematode (SCN, H. glycines). Vegetable soybean, or edamame, has become a major exporting agricultural product in Taiwan with an annual revenue over $80 million USD since 2017. Several local varieties have been developed to fulfill the market needs such as the traits of flavor and sweetness. However, it remains unclear if the historical breeding programs ever incorporated rhg1 resistance into the varieties of Taiwan. This study applied the TaqMan qPCR method to measure the fluorescent signals specific to the rhg1 locus on the chromosome 18 of soybean, and the ratio of VIC and FAM signals were analyzed to predict the rhg1 copy number in the 21 soybean varieties of Taiwan. The results indicated the copy number and the single nucleotide polymorphisms of the 21 soybean varieties were identical to the susceptible soybean variety ‘Williams 82’. As importation of soybean will be continuously needed to fulfill the market and because SCN is absent in the soybean fields of Taiwan, lacking rhg1 resistance in the local soybean varieties may put the edamame industry at risk and early implementation of SCN resistance in the breeding program, alongside the application of quarantine regulations, will be the key to maintain the SCN-free status and to sustain the edamame industry in Taiwan.

Pierce's disease (PD) of grapevine is caused by the bacterium Xylella fastidiosa. In this study, an integrated approach was applied to assess PD susceptibility among different Vitis vinifera cultivars that incorporated disease severity, bacterial pathogen abundance and loss of stem xylem hydraulic conductivity. It was hypothesized that levels of PD susceptibility in V. vinifera can be attributed in part to the host anatomical features that are shaped by its pedigree background. Two popular wine grape cultivars were initially selected from the occidentalis group, Merlot and Cabernet Sauvignon, and one from the orientalis group, Thompson Seedless. The more recently bred table grape cultivar Scarlet Royal, that has mixed pedigree parentage, was also included. PD susceptibility was compared to the known PD resistant b43-17 V. arizonica/candicans wild grape species from North America. The data indicated that Thompson Seedless was ranked as the most susceptible to PD because it significantly exhibited the most severe disease symptoms at 12 weeks post-inoculation and hosted the highest X. fastidiosa titre of the cultivars, and lost over 90% of its stem hydraulic conductivity. In contrast, the other three cultivars displayed less susceptibility to PD. The way in which the xylem anatomy could impact PD susceptibility in V. vinifera cultivars is discussed, together with how grape pedigrees and their cognate centre of domestication may have influenced xylem anatomical features. This work provides a reference framework to further test the hypothesis that V. vinifera cultivars with wide xylem vessels may be more prone to PD decline.

Aphelenchoides besseyi is a seed-borne plant-parasitic nematode pathogen that causes rice white-tip disease worldwide. For quarantine purposes at custom border inspection and in field surveillance, a rapid, highly specific, and sensitive loop-mediated isothermal amplification (LAMP) assay for the nematode detection was developed. The assay targets the sequence variable region of the mitochondrial cytochrome oxidase subunit I (COI) gene of the nematode. It is capable of distinguishing the A. besseyi rice pathotype from the closely related A. besseyi nest fern pathotype. The assay is highly sensitive, with the detection minimum limit at 103 copy numbers/µl cloned target plasmid or a single nematode crude DNA. A minimum of 35 min is needed for the assay to complete, and the detection results can be rapidly determined by the color change of hydroxynaphathol blue dye or by the indication bar on a specific lateral flow dipstick. The application potential of this assay on rice seeding was demonstrated at the sensitivity level of five nematodes in single rice seedling. This is the first LAMP assay for A. besseyi rice race detection using a mitochondria gene as marker. This assay is well-suited for phytosanitary examination and seedling screening purposes in nurseries.

Pratylenchus vulnus was discovered in nematode-distributing fields from symptomatic seedling roots and corresponding rhizosphere soil on strawberry farms in Taiwan. Microscopic measurements and scanning electron microscope observations of both sexes of the nematode coincided with the general morphological descriptions of the species. Four different types of female tail termini were observed, including pointed, digitate, smooth and tapering. Molecular analysis of the ribosomal RNA sequence (SSU, ITS and LSU regions) and the mitochondria COI gene sequences confirmed the species identification. Phylogenetic analysis suggested no specific geographic linkage of the Taiwan population to other previously reported populations.

Barley yellow dwarf virus is a group of positive-sense single stranded RNA viruses with many species belonging to the family Luteoviridae and known to cause significant yield losses of cereal crops worldwide (Irwin and Thresh 1990). Oat (Avena sativa L.), a temperate cereal crop usually grown as forage in subtropical regions, has been recently reintroduced into Taiwan as a local winter forage source. In April 2017, yellowing, V-shape reddening, and purple symptoms were observed on 7.9% of the mature leaves of the oat plants grown in the experimental field of National Taiwan University (NTU) in Taipei city, Taiwan. We collected 37 leaf samples with suspected virus-infection symptoms in the experimental field for virus screening. The samples were expressing varying degrees of yellowing, browning, or typical barley yellow dwarf virus (BYDV)-associated V-shape reddening and purple symptoms. An additional five samples with no symptoms were also collected. These 37 samples belong to 22 oat lines, including two registered cultivars and 20 unreleased breeding lines. Some lines were replicated in the field and therefore were sampled more than once. A specific reverse transcription polymerase chain reaction assay (RT-PCR) for BYDV, covering the coat protein (CP) gene and partial RNA-dependent RNA polymerase regions, was performed with the primers Shu-F (5′-TACGGTAAGTGCCCAACTCC-3′) and Yan-R (5′-TGTTGAGGAGTCTACCTATTTG-3′) on the extracted total RNA of the samples (Malmstrom and Shu 2004). Among the examined samples, only the three expressing typical BYDV symptoms tested positive, whereas the other 34 samples with solely yellowing or browning symptoms and the five symptomless samples tested negative. The samples belonged to the cultivar Swan and two breeding lines, 15-39 and 16-47; the seeds of the three symptomatic oats were all imported from the United States. We further cross-examined the three positive samples with another RT-PCR assay, using specific primer pairs targeting the BYDV CP gene (for strains PAV, MAV, and GAV): Luteo1F (5′-TTCGGMSARTGGTTGTGGTCCA-3′) and YanR-new (5′-TGTTGAGGAGTCTACCTATTTNG-3′) (Mustafayev et al. 2013; Svanella-Dumas et al. 2013). The electrophoresis analysis of the RT-PCR amplicons revealed the expected 545-bp fragment from all. The amplicons were later cloned into pCR2.1-TOPO (Invitrogen, Carlsbad, CA) for sequencing analysis. All of the sequences obtained were identical (GenBank accession nos. MF618251, MK361042, and MK361043) and showed 99% similarity to the BYDV-PAV isolates from the United States (accession nos. EF521840 and DQ115532) in GenBank. Based on the phylogenetic analysis of CP gene sequences, the BYDV-PAV Taiwan isolates and these two U.S. isolates were in the same cluster. To further confirm the results, the BYDV-PAV specific enzyme-linked immunosorbent assay on the three symptomatic samples, using the commercialized kit (Agdia, Elkhart, IN), also aligned with the prior assay and showed positive reaction results. To our knowledge, this is the first report of BYDV-PAV in Taiwan. The phylogeny analysis of the virus suggests the BYDV-PAV might have been introduced through the seeds, which had gone through one cycle of multiplication at the border between Idaho and Oregon states prior to growing in Taiwan. Because the BYDV infection on oat presented a threat to cereal crop production in Taiwan, all oat plants in the NTU experimental field were eliminated immediately to prevent the spread of the disease. Agricultural agencies were informed of the incidence, and oat growers were educated to identify the BYDV symptoms on oat. Further field surveys of BYDV on the alleged vector insects will be carried to better understand the disease biology in Taiwan and to provide information on the disease system in the Southeast Asia region.

Replant diseases often occur when pome and stone fruits are grown in soil that had previously been planted with the same or similar plant species. They typically lead to reductions in plant growth, crop yield and production duration. In this project, greenhouse assays were used to identify a peach orchard soil that caused replant disease symptoms. Biocidal treatments of this soil led to growth increases of Nemaguard peach seedlings. In addition, plants grown in as little as 1% of the replant soil exhibited reduced plant growth. These results suggest that the disease etiology has a biological component. Analysis of roots from plants exhibiting various levels of replant disease symptoms showed little difference in the amounts of PCR-amplified bacterial or fungal rRNA genes. However, analysis using a stramenopile-selective PCR assay showed that rRNA genes from this taxon were generally more abundant in plants with the smallest top weights. Nucleotide sequence analysis of these genes identified several phylotypes belonging to Bacillariophyta, Chrysophyceae, Eustigmatophyceae, Labyrinthulida, Oomycetes, Phaeophyceae and Synurophyceae. Sequence-selective quantitative PCR assays targeting four of the most abundant phylotypes showed that both diatoms (Sellaphora spp.) and an oomycete (Pythium ultimum) were negatively associated with plant top weights.

Background PRISE2 is a new software tool for designing sequence-selective PCR primers and probes. To achieve high level of selectivity, PRISE2 allows the user to specify a collection of target sequences that the primers are supposed to amplify, as well as non-target sequences that should not be amplified. The program emphasizes primer selectivity on the 3’ end, which is crucial for selective amplification of conserved sequences such as rRNA genes. In PRISE2, users can specify desired properties of primers, including length, GC content, and others. They can interactively manipulate the list of candidate primers, to choose primer pairs that are best suited for their needs. A similar process is used to add probes to selected primer pairs. More advanced features include, for example, the capability to define a custom mismatch penalty function. PRISE2 is equipped with a graphical, user-friendly interface, and it runs on Windows, Macintosh or Linux machines. Results PRISE2 has been tested on two very similar strains of the fungus Dactylella oviparasitica, and it was able to create highly selective primers and probes for each of them, demonstrating the ability to create useful sequence-selective assays. Conclusions PRISE2 is a user-friendly, interactive software package that can be used to design high-quality selective primers for PCR experiments. In addition to choosing primers, users have an option to add a probe to any selected primer pair, enabling design of Taqman and other primer-probe based assays. PRISE2 can also be used to design probes for FISH and other hybridization-based assays.

Ataxia-telangiectasia is a genetic disorder associated with high incidence of B-cell lymphoma. Using an ataxia-telangiectasia mouse model, we compared lymphoma incidence in several isogenic mouse colonies harboring different bacterial communities, finding that intestinal microbiota are a major contributor to disease penetrance and latency, lifespan, molecular oxidative stress, and systemic leukocyte genotoxicity. High-throughput sequence analysis of rRNA genes identified mucosa-associated bacterial phylotypes that were colony-specific. Lactobacillus johnsonii, which was deficient in the more cancer-prone mouse colony, was causally tested for its capacity to confer reduced genotoxicity when restored by short-term oral transfer. This intervention decreased systemic genotoxicity, a response associated with reduced basal leukocytes and the cytokine-mediated inflammatory state, and mechanistically linked to the host cell biology of systemic genotoxicity. Our results suggest that intestinal microbiota are a potentially modifiable trait for translational intervention in individuals at risk for B-cell lymphoma, or for other diseases that are driven by genotoxicity or the molecular response to oxidative stress. Cancer Res; 73(14); 4222–32. ©2013 AACR.

Background Replant disease often occurs when certain crops are “replanted” in a soil that had previously supported the same or similar plant species. This disease typically leads to reductions in plant growth, crop yields, and production duration, and its etiology remains ill-defined. The objective of this study was to identify microorganisms associated with peach replant disease symptoms at a field location in California, USA. Soil samples were subjected to treatments to create various levels of replant disease symptoms. Clonal peach seedlings were grown in the treated soils in greenhouse trials. After 6 weeks, plant growth parameters were measured, and both culture and culture-independent analyses were performed to identify root-associated bacteria, fungi and stramenopiles. Results A total of 295,785 bacterial operational taxonomic units (OTU) were identified by an Illumina-based, high throughput sequence analysis of rRNA genes. Among the 60 most abundant OTUs, 27 showed significant (P