Phytobiomes Journal
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Phytobiomes Journal
@phytobiomesjournal.bsky.social
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Phytobiomes Journal (est. 2016) is a gold open access journal from The American Phytopathological Society, publishing research on plant-associated organisms and ecosystems.
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“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. 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.
January 20, 2026 at 4:53 PM
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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. Overview of study design.
January 13, 2026 at 5:13 PM
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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. 1. Mesocosm experimental system.
January 6, 2026 at 4:51 PM
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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. 2. Effect of bacterial strains on Botrytis cinerea lesion formation.
December 30, 2025 at 5:13 PM
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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. 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.
December 23, 2025 at 5:05 PM
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“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. 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.
December 17, 2025 at 8:05 PM
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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
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.
December 12, 2025 at 9:09 PM
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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
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 ...
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December 9, 2025 at 5:11 PM
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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
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.
December 2, 2025 at 5:05 PM
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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
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...
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November 26, 2025 at 6:56 PM
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“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/...
November 21, 2025 at 4:56 PM
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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
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.
November 24, 2025 at 5:06 PM
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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
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...
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November 19, 2025 at 8:09 PM
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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
Fig. 1. Schematic representation of the experimental design used to assess the impact of host plant species change or virus infection.
November 14, 2025 at 8:54 PM
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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
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...
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November 11, 2025 at 4:50 PM
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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
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.
November 6, 2025 at 9:07 PM
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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
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...
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November 3, 2025 at 5:13 PM
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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. 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.
October 29, 2025 at 7:52 PM
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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. 9. Comparison of the pathogenicity of strains Z6, 2CM2G-5, TB1, and SW1 with that of an uninoculated control plant (CK).
October 24, 2025 at 8:52 PM
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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
Fig. 1. Diversity of leaf symbiotic structures.
October 21, 2025 at 4:55 PM
Reposted by Phytobiomes Journal
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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

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October 16, 2025 at 2:14 PM
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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
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).
October 14, 2025 at 4:52 PM
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Editor’s Pick: “Bacterial Auxin Production in the Phyllosphere,” by Lorena I. Rangel et al. Read the article in Volume 9, Number 3 of Phytobiomes Journal: https://doi.org/10.1094/PBIOMES-02-25-0010-R
Fig. 4. Phylogenetic tree based on the alignment of partial 16S rRNA gene sequences from the 235 bacterial isolates that were collected from lettuce leaf samples at 38 or 67 days after planting (dap). Clades are colored according to taxon membership, down to the genus level, as per alignment with RDP type strains. An open circle next to the name of an isolate indicates that the isolate came from a 67-dap leaf sample. A black dot indicates that the isolate tested as a high producer of indole-3-acetic acid.
October 7, 2025 at 5:08 PM
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Editor’s Pick: Terrence H. Bell et al. believe that there is no single “best” approach to iterative microbiome passaging but that experimental design choices can have substantial impacts on outcomes. Learn more: https://doi.org/10.1094/PBIOMES-11-24-0113-P
Fig. 1. Here, we visualize how the impact of iterative microbiome passaging may differ with time.
September 30, 2025 at 6:50 PM
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Silvia Talavera-Marcos et al. examined tomato rhizosphere microbiome assembly and potential composition–function links using a framework based on phylogenetically constrained microbial community assembly. https://doi.org/10.1094/PBIOMES-10-24-0098-SC
Coupled Phylogenetic and Functional Enrichment in the Tomato Rhizosphere Microbiome | Phytobiomes Journal
Plant–microbe interactions occur mainly in the rhizosphere, a hot spot of microbial activity and diversity, and the outcome of these interactions can significantly affect plant productivity. A better understanding of the rhizosphere microbiome is, there...
doi.org
September 24, 2025 at 7:48 PM