Phytobiomes Journal

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

Fig. 1. Overview diagram of key themes and unknowns about endohyphal bacteria within the phytobiome, based on studies covered within this review. The metabolite exchanges and outcomes are representative of observed possibilities across diverse organisms and are not necessarily all true for any given single endohyphal symbiosis.

Dallas Moses and Morgan Carter compiled studies of endohyphal bacteria (EHB) from across diverse plant-associated microbes to provide a primer for EHB studies, considered through a phytobiomes lens, and comment on the directions of this emerging field: https://doi.org/10.1094/PBIOMES-12-24-0117-MRVW

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

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

Fig. 1. Diversity of leaf symbiotic structures.

Léa Ninzatti, Marie-Françoise Jardinaud, and Aurélien Carlier review current knowledge of hereditary leaf symbiosis in tropical plants and explore hypotheses regarding mechanisms that enable these highly specific interactions: https://doi.org/10.1094/PBIOMES-11-24-0111-RVW

On this #WorldFoodDay, we celebrate the efforts of those who nourish our communities, protect our planet, and shape a better future through better food for all. Explore resources to learn more about food security and sustainability. #FAO80

https://bit.ly/4nqN3x7

Fig. 1. Scheme of samples taken and parameters analyzed 56 days after planting apple genotypes M.26, EMR.2, G.202, and G.935 (rootstocks) and Malus spectabilis MAL0130 and M. sargentii MAL0739 (wild-type accessions) in soils from six different apple replant disease (ARD)-affected sites: HG, Heidgraben; HO, Holm; EH, Ellerhoop; PI, Pillnitz; RU, Ruthe; ME, Meckenheim. The soils were either untreated (ARD) or γ-irradiated (γARD).

Editor’s Pick: Findings from Kristin Hauschild et al. highlight that apple replant disease (ARD) tolerance in apple genotypes is linked to the soil microbiome and other soil properties, indicating the need for an integrated approach to management: https://doi.org/10.1094/PBIOMES-08-24-0082-R