Fig. 1. In experiment 1, we grew maize with agricultural, prairie, or sterile control inocula under controlled growth chamber settings. After 4 weeks of growth, better-parent heterosis (BPH) was greatest in the second agricultural soil for A, stem diameter and greatest in the second prairie soil for B, week-4 chlorophyll concentration. Points show the estimated marginal mean (EMM) values for each genotype in each soil, and error bars show the standard error for the EMMs (Dunnett's test: ns = not significant, P > 0.05; * = P < 0.05; ** = P < 0.01; *** = P < 0.001). C, BPH was calculated for soil inoculum using EMM values for stem diameter and week-4 chlorophyll concentration. The observed ΔBPH is shown as a vertical red line, and the histogram shows the distributions of ΔBPH for 999 permutations of the data with respect to soil inocula.

To further understand how microbes influence heterosis, Kayla M. Clouse et al. characterized variation in maize heterosis when grown in soil inocula derived from historical maize farms or prairies: https://doi.org/10.1094/PBIOMES-04-25-0026-R

Fig. 1. Pictures of the sampling. A, Vitis vinifera ‘Sauvignon blanc’ expressing esca leaf symptoms, from which we sampled petioles from B, symptomatic or C, asymptomatic leaves; D, wood tissues from the xylem showing a brown stripe (red arrow); different wood tissues collected from E, a trunk cross section, on which healthy wood (HW), black necrosis (BN), and white rot (WR) were visible; and 1-year-old (stems) and 2-year-old (canes) shoots that were not photographed. F, V. vinifera ‘Sauvignon blanc’ under water deficit, from which we sampled petioles from G, leaves; different wood tissues collected from H, a trunk cross section, on which HW and BN are visible, and 1-year-old (stems) and 2-year-old (canes) shoots (not photographed). Similarly, we sampled the same types of tissue from control well-watered asymptomatic plants (not shown).

Results from Pierre Gastou et al. indicate that drought increased #Ascomycota pathogen abundance in grapevine trunk but did not increase wood degradation and esca expression. Learn more: https://doi.org/10.1094/PBIOMES-07-25-0048-R

Fig. 1. Experimental design. Left panel illustrates the experimental field site, with each 24 × 29-m box representing 11 unique cover crop treatments plus a weeded fallow plot, and adjacent rows of corn and soybean crops. Arrows at the top indicate the annual crop rotation within an entry, which is four times replicated in a randomized block design. Within plots, each “x” denotes a microbial trap deployed in each year. The right panel provides a timeline of events during each year of the study.

Sarah C. Richards et al. investigated the influence of various cover crop treatments on soil microbial community assembly using an in-situ microbial trap design to isolate recolonizing microorganisms from the bulk soil microbial seedbank: https://doi.org/10.1094/PBIOMES-07-25-0054-R @PSUecosystems

Fig. 8. Correlation network of microbial taxa based on cooccurrence analysis in sandy soil A, root and B, rhizosphere microbiomes and clay soil C, root and D, rhizosphere microbiomes. Nodes represent microbial taxa present at a relative abundance ≥ 0.5% across the entire dataset. Node size corresponds to mean relative abundance, and node labels indicate operational taxonomic unit identification. Edges represent significant pairwise correlations determined by Spearman's rank correlation. Red edges denote significant negative correlations, and blue edges represent significant positive correlations. Only edges with absolute correlation coefficient |r| ≥ 0.6 are shown. The node corresponding to Dactylonectria macrodidyma is highlighted in green.

Catarina Leal et al. investigated the impact of #Dactylonectria macrodidyma on fungal community dynamics in grapevines grown in sandy and clay soils, highlighting how soil properties influence pathogen-induced changes in fungal community structure: https://doi.org/10.1094/PBIOMES-06-25-0042-R

Fig. 2. Relative abundance of the seven most common species found across all three metabarcoding datasets. Relative abundance was calculated as the number of reads per species out of the total number of reads assigned a taxonomic label to the species level.

Industrial hemp was a historically important fiber crop prior to the U.S. federal regulation of marijuana in the early 20th century. Jaime E. Blair et al. provide an important resource for #oomycete identification and industrial hemp management practices: https://doi.org/10.1094/PBIOMES-07-25-0056-R

Fig. 1. A, Relative percent abundances of the top five fungal phyla across all samples. Phyla with abundances below 5% were not plotted. B, The respective top five fungal families occurring within contaminated and noncontaminated sites. For plants in the noncontaminated site, only four fungal families had relative abundances >40%. C, Top 10 fungal guild compositions (raw abundances) between contaminated and noncontaminated sites. Unassigned guild, which comprises most of the fungal taxa, were not depicted in the plot for better resolution.

Short Communication: “Host Plant Traits and Site History Shape Root Fungal Endophytic Communities of Sporobolus spartinae After Long-Term Exposure to Contaminants,” by Candice Y. Lumibao, Yue Liu, and Ioana E. Pavel. Learn more: https://doi.org/10.1094/PBIOMES-06-25-0045-SC

Fig. 1. The scheme of generating and testing rhizosphere microbial inoculants in this study. Soybean cyst nematode (SCN)-susceptible cultivars were Dickey, Rolette, IA2104RA12, IA3054RA12, and Williams 82; SCN-resistant cultivars were ND17-22117, ND17-20565, IAR1903SCN, IAR2801SCN, and Jack.

New findings from Chuntao Yin and Nathan Lahr demonstrate that soybeans recruit beneficial soil microbes to defend against the devastating soybean cyst #nematode. Read the press release to learn more: https://bit.ly/4cw2v9d

Read the original article: https://bit.ly/3NmjBfv @plantdisease.bsky.social

Fig. 1. Summary of project workflow. Potato phyllosphere bacteria and tuber endophytes were sampled from field-grown plants. Isolated native potato bacterial strains were individually introduced to axenic potato plantlets in vitro. The resulting bacterized plants were grown in the greenhouse to assess the effects and persistence of the endophytes. Figure created using BioRender.

José A. Sánchez-Gallego et al. hypothesized that introducing natural potato endophytic bacteria to plantlets in tissue culture could increase seed potato minitubers. Learn more: https://doi.org/10.1094/PBIOMES-05-25-0036-R

Fig. 1. Pectobacterium species diversity in raw reads (left panel) and in samples where potato reads were removed (right panel). The number on the top of each bar indicates millions of reads assigned to the genus Pectobacterium. The reads were classified using the PectoDB with Kraken2.

Short Communication: “Metagenomic and Culture-Based Detection of Pectobacterium spp.: What You See Is Not Always What You Get,” by Sadie M. Seaman et al. Learn more: https://doi.org/10.1094/PBIOMES-09-24-0085-SC

A plant ‘vaccine’ takes on corn rootworm, a fearsome pest Inoculating soil with pink microbes could help reduce the use of toxic insecticides.

Damage from corn rootworm costs an excess of $1 billion each year in the United States alone. Man P. Huynh et al. may have found a solution: doi.org/10.1094/PBIO...

Read the @science.org article to learn more: www.science.org/content/arti...

@plantdisease.bsky.social

Fig. 1. A, Maximum likelihood phylogenetic tree of 23 conifer species grown in the phylosymbiosis experiment (with outgroup Betula pendula) alongside B, varying plant traits and soil physicochemical properties (z-transformed) measured after growing for approximately 52 weeks in a common soil. Values on branches in A show bootstrap support on the left (0 to 100) and posterior probabilities on the right for each split.

Natalie J. Graham et al. present evidence for phylosymbiosis in the root systems of conifer seedlings in both bacterial and fungal communities. Learn more: https://doi.org/10.1094/PBIOMES-03-25-0022-R

Fig. 9. Comparison of the pathogenicity of strains Z6, 2CM2G-5, TB1, and SW1 with that of an uninoculated control plant (CK).

“Omics-Based Insights into Microbial Community Changes and Pathogen Identification in Strawberries Under Continuous Cropping,” by Chi Zhang et al. Learn more: https://doi.org/10.1094/PBIOMES-04-25-0027-R

Fig. 1. A, Healthy uninoculated Dwarf Cavendish banana plant. B, Early symptomatic infection of Fusarium oxysporum f. sp. cubense wilt in infected Dwarf Cavendish banana.

Vanessa E. Thomas et al. identified and differentiated Fusarium oxysporum f. sp. cubense tropical race 4 pathobionts from microbiota under dysbiosis during infection. Learn more about the findings: https://doi.org/10.1094/PBIOMES-10-24-0097-R @SanTonyB

Fig. 3. A, Mean percentage of Theobroma cacao pods infected with frosty pod rot (FPR) and B, percentage of pods with sporulating lesions of Moniliophthora roreri following eight monthly inoculations with endophytic fungi at La Magnita farm, Bocas del Toro, Panama. Treatments included an untreated control, Waltergamsia zeylanica (TCF 400), and Clonostachys rosea (TCF 417). Letters above points indicate Tukey-adjusted pairwise significance groups (P < 0.05) within each genotype.

“The Interplay of Theobroma cacao Genetics and Its Pod Mycobiome on Controlling Pathogenic Fungus Moniliophthora roreri,” by Hilda E. Castillo et al. Read the open access article to learn more: https://doi.org/10.1094/PBIOMES-02-25-0009-R

Fig. 1. Overview of study design.

Larissa Carvalho Ferreira et al. investigated the mycobiome composition associated with tar spot disease in corn and to evaluate the genetic diversity of Phyllachora maydis in Florida: https://doi.org/10.1094/PBIOMES-12-24-0118-R

Fig. 1. Mesocosm experimental system.

Editor’s Pick: Josh Sumner et al. investigated whether large mesocosms could be used to study the 3D spatial patterning of microbes and correlated metabolites across mature corn root systems to improve microbial-based products. Learn more: https://doi.org/10.1094/PBIOMES-09-24-0088-R @becky_bart

Fig. 2. Effect of bacterial strains on Botrytis cinerea lesion formation.

Editor’s Pick: Mackenzie Eli William Loranger et al. report the establishment of a screening method and the identification of 13 immunity-inducing strains in tomato plants, including a strain of Chitinophaga arvensicola. Learn more: https://doi.org/10.1094/PBIOMES-01-25-0004-R @DezielEric

Fig. 1. Experimental design. A, We split 80 plants evenly between eight treatment groups using four different inoculants (none, sterile water, B. amyloliquefaciens, whole natural community) and two different environments (drought, watered). B, We quantified plant health by collecting nine response variables.

Editor’s Pick: Jacob A. Heil et al. used Artemisia tridentata subsp. tridentata to measure the response of seedlings to microbial inoculations and drought conditions. Learn more: https://doi.org/10.1094/PBIOMES-04-25-0029-R

Fig. 3. Local indicator of phylogenetic association (local Moran's I) for genera autocorrelated with heritability in switchgrass. Significant associations between tree position and heritability are in red.

“Bacterial Assembly in the Switchgrass Rhizosphere Is Shaped by Phylogeny, Host Genotype, and Growing Site,” by Jeremy Sutherland et al. Read the article in Volume 9, Number 3 of Phytobiomes Journal: https://doi.org/10.1094/PBIOMES-12-24-0116-R

Fig. 1. Map of the study area in Minas Gerais State of Brazil on the left and, on the right, a representation of coffee root sites enclosed by a red line with red and blue dots pointing out symptomatic and asymptomatic sampling plants. WGS84 (World Geodetic System) is a global reference system, and UTM zone (Universal Transverse Mercator) is a coordinate system.

Root-knot nematode egg masses host distinct bacterial communities, according to research by Daniele de Brum et al. Significant differences were found in the communities colonizing symptomatic and asymptomatic plants in field conditions: https://doi.org/10.1094/PBIOMES-10-24-0099-R

The Interaction Between Abiotic and Biotic Soil Factors Modulates Heterosis Expression in Maize | Phytobiomes Journal Heterosis, or hybrid vigor, refers to the phenotypic superiority of hybrids relative to their parental inbred lines. Recent work showed that manipulation of the soil microbial community consistently altered heterosis but the direction of the effect was ...

Get a First Look 🔍 “The Interaction Between Abiotic and Biotic Soil Factors Modulates Heterosis Expression in Maize,” by Kayla M. Clouse et al.: https://doi.org/10.1094/PBIOMES-04-25-0026-R

Fig. 2. Heatmap of soybean rhizosphere microbial genera significantly influenced by the growth stage (hash) and cover crops (stars) based on analysis of variance of log2(1 + x)-transformed sequence counts and clustered based on complete-linkage hierarchical clustering of Euclidean distances. Colored bars at the right top of the graph present the growth stage and cover crop treatments for each sample (A, bacterial genera; B, fungal genera) without considering cover crop treatment.

Cover crop legacies may promote beneficial changes in cash crop rhizosphere microbiota. Read the article by Chuntao Yin, Shannon L. Osborne, and R. Michael Lehman to learn more: https://doi.org/10.1094/PBIOMES-09-24-0086-R

Shifting Fungal Networks: How Dactylonectria macrodidyma Shapes Grapevine Mycobiome in Diverse Soils | Phytobiomes Journal This study investigates the impact of Dactylonectria macrodidyma on fungal community dynamics in grapevines grown in sandy and clay soils, highlighting how soil properties influence pathogen-induced changes in fungal community structure. High-throughput...

Get a First Look 🔍 “Shifting Fungal Networks: How Dactylonectria macrodidyma Shapes Grapevine Mycobiome in Diverse Soils,” by C. Leal et al.: https://doi.org/10.1094/PBIOMES-06-25-0042-R

“Characterization of Immunity-Inducing Rhizobacteria Highlights Diversity in Plant–Microbe Interactions” by Mack Loranger in the Yoshioka Lab is the Editor’s Pick in @phytobiomesjournal.bsky.social! Congratulations! 🧪🌱 #PlantScience #SoilScience apsjournals.apsnet.org/doi/10.1094/...

Fig. 5. Composition of the root-associated fungal endophytic community of potato plants in samples grown in three different growing conditions: GER soil representing Germany, NL soil representing the Netherlands, and in vitro conditions. The relative abundances (%) are calculated for major fungal endophytic families present in the 11 potato cultivars (n = 3). Taxa are shown at the nearest classified level when family-level classification was unavailable.

Understanding the roles of endophytes in sustainable agriculture is a key focus of research. Jyotsna Nepal et al. investigated how 11 potato cultivars and 3 different growing conditions influence the diversity of microbial endophytes in potato roots: https://doi.org/10.1094/PBIOMES-08-24-0083-R

Host Plant Traits and Site History Shape Root Fungal Endophytic Communities of Sporobolus spartinae After Long-Term Exposure to Contaminants | Phytobiomes Journal Root fungal endophytes (fungi inhabiting the inside of root cells without any apparent harm) are widely recognized as important symbionts of host plants, providing benefits to the host plant such as water and nutrient acquisition. While endophyte commun...

Get a First Look 🔍 “Host Plant Traits and Site History Shape Root Fungal Endophytic Communities of Sporobolus spartinae After Long-Term Exposure to Contaminants,” by Candice Y. Lumibao, Yue Liu, and Ioana E. Pavel: https://doi.org/10.1094/PBIOMES-06-25-0045-SC

Fig. 1. Schematic representation of the experimental design used to assess the impact of host plant species change or virus infection.

New research from Celia de Moya-Ruiz et al. underlines shifts in the #aphid microbiome, which could provide insights for further investigation of microbial resource-based solutions to control aphid pests and associated viral diseases in agriculture: https://doi.org/10.1094/PBIOMES-03-25-0017-R

Diversity of Soilborne Oomycetes Associated with Industrial Hemp in Southeastern Pennsylvania: A Comparison of Metabarcoding Loci for Taxonomic Profiling | Phytobiomes Journal Industrial hemp was historically important as a fiber crop in Pennsylvania prior to the U.S. federal regulation of marijuana in the early 20th century. The recent reestablishment of industrial hemp production, especially for cannabidiol extracts, necess...

Get a First Look 🔍 “Diversity of Soilborne Oomycetes Associated with Industrial Hemp in Southeastern Pennsylvania: A Comparison of Metabarcoding Loci for Taxonomic Profiling,” by Jaime E. Blair et al.: https://doi.org/10.1094/PBIOMES-07-25-0056-R

Fig. 2. Presence and absence of bacterial genes that influence plant hormone production or are known virulence factors in pathogenic Agrobacterium fabrum. Bacterial isolates are arranged on the vertical axis and genes on the horizontal axis. The legend shows whether a given gene is involved in plant hormone production or virulence.

Nicholas R. LeBlanc et al. characterized a novel endophytic #Agrobacterium sp. El2ro-1b from strawberry by generating and analyzing a high-quality genome assembly and testing the effects of the endophyte on plant growth: https://doi.org/10.1094/PBIOMES-01-25-0003-SC

The Interplay of Theobroma cacao Genetics and Its Pod-Mycobiome on Controlling Pathogenic Fungus Moniliophthora roreri | Phytobiomes Journal The tropical tree crop Theobroma cacao has many cultivars that differ genetically and show differences in resistance to disease. These cultivars also host diverse microbiomes, including endophytic fungi, with capacity to protect the plant against diseas...

Get a First Look 🔍 “The Interplay of Theobroma cacao Genetics and Its Pod-Mycobiome on Controlling Pathogenic Fungus Moniliophthora roreri,” by Hilda E. Castillo et al.: https://doi.org/10.1094/PBIOMES-02-25-0009-R