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Phytobiomes Journal

@phytobiomesjournal.bsky.social

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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Phytobiomes Journal @phytobiomesjournal.bsky.social · last mo.

“Diverse Pseudomonas Species Engage in Beneficial and Suppressive Interactions with the Kiwifruit Pathogen Pseudomonas syringae pv. actinidiae Across Actinidia Germplasm,” by Haileigh R. Patterson et al. Learn more: https://doi.org/10.1094/PBIOMES-08-25-0071-R #microbiome #Pseudomonas

Fig. 7.
Results of real-time qPCR analysis of the virulence of germplasm isolates in competition with Pseudomonas syringae pv. actinidiae (Psa) on Actinidia arguta at 7 days postinoculation (dpi). Plantlets were flooded with 106 CFU/ml of each bacterial isolate. Bacterial growth was quantified by real-time qPCR using isolate-specific primers and normalizing the cycle threshold (Ct) to a plant housekeeping gene, EF1α, to get a ΔCt value.

Phytobiomes Journal @phytobiomesjournal.bsky.social · 2mo ago

Shuxian Li et al. present the first-known multiyear, field-based study of soybean seed endophytic microbiomes and the impact of seedborne pathogen inoculation: https://doi.org/10.1094/PBIOMES-08-25-0070-R #soybean #seedmicrobiome #microbiome

Fig. 6.
Significant associations (q < 0.05) between fungal amplicon sequence variants (ASVs) and environmental and seed factors. Positive associations are shown in red and negative associations in blue.

Phytobiomes Journal @phytobiomesjournal.bsky.social · 2mo ago

Christopher James Barnes et al. suggest that the aboveground and belowground microbial communities are interconnected, with the soil serving as a reservoir for aboveground microbes but only to a limited extent. Learn more: https://doi.org/10.1094/PBIOMES-08-25-0060-R #metabolomics #microbiome

Phytobiomes Journal @phytobiomesjournal.bsky.social · 2mo ago

“Does Emerald Ash Borer Infestation Alter Ash Phloem Microbial Communities over Time?” Read the article by Andrew J. Mann et al. to find out: https://doi.org/10.1094/PBIOMES-06-25-0046-R #plantmicrobiome #microbiome #endophytes #emeraldashborer

Fig. 1.
A sampling overview diagram. Trees are organized into infestation categories based on the following criteria. A: Emerald ash borer (EAB)-infested phloem in the bottom 2 m of the tree during the entire study period. B: EAB-infested phloem is absent in the bottom 2 m of the tree at the start of the study but present at the end of the study. C: Trees show symptoms of EAB infestation in canopy but no EAB-infested phloem in the bottom 2 m of the tree. D: No symptoms of EAB infestation. The orange in the figure provides a simplified representation of the locations of EAB galleries within the tree in each infestation category. The control phloem samples are labeled as CP, uninfested phloem before EAB reached the base of the tree is labeled as UP Before, uninfested phloem after EAB reached the base of the tree is labeled as UP After, infested phloem is labeled as IP, frass is labeled as F, and the larval samples are labeled as La.

Phytobiomes Journal @phytobiomesjournal.bsky.social · 2mo ago

Using data from rhizosphere soil from 95 field-grown sunflower inbred lines, Clifton P. Bueno de Mesquita et al. found that heritable genetic differences affect sunflower rhizosphere archaeal, bacterial, and fungal communities across all taxonomic levels: https://doi.org/10.1094/PBIOMES-05-25-0034-R

Fig. 6.
Sloan's neutral model for A, archaea/bacteria and B, fungi. In both datasets, only zero-radius operational taxonomic units (ZOTUs) with at least 15 reads across the whole dataset were included (n = 10,522 and 1,425, respectively). Inset pies show the proportion of ZOTUs that were above (positive selection), below (negative selection), or in (no selection) the neutral model. The solid blue line represents the best fit to the neutral model, and the dashed blue lines are the 95% confidence intervals. The R2 is the fit to the neutral model, and the Nm is the metacommunity size times immigration.

Phytobiomes Journal @phytobiomesjournal.bsky.social · 2mo ago

Results from Hayden W. Bock et al. indicated that groundcovers modulate bacterial and fungal composition in vineyard soil microbiomes within and beyond their rooting zones. Learn more: https://doi.org/10.1094/PBIOMES-11-25-0087-SC #microbiome

Fig. 1.
Grass groundcovers have denser, shallower root systems than grapevines. When planted in vineyards, grapevines redistribute roots deeper to avoid competition. This results in more roots overall, with substantial groundcover roots at shallow depths and grapevine roots beyond the groundcover root zone. This figure demonstrates our hypothesis that groundcovers promote a more diverse and compositionally distinct bulk-soil microbiome, favoring decomposer taxa associated with increased soil carbon inputs. We expected these effects to be greatest near the surface, where grass roots dominate, and diminish with depth.

Phytobiomes Journal @phytobiomesjournal.bsky.social · 2mo ago

Anna-Katharina Garrell et al. report the development of a defined minimal growth medium for a well-characterized seven-member maize root synthetic microbial community. Learn more: https://doi.org/10.1094/PBIOMES-07-25-0053-SC #maize #syncom #plantmicrobiome

Fig. 2.
Growth of synthetic community species in 0.5× Murashige and Skoog, glucose, and malate augmented with additional amino acids and vitamins (n = 3).

Phytobiomes Journal @phytobiomesjournal.bsky.social · 3mo ago

Editor’s Pick: “Contribution of Floral Transmission to the Assembly and Health Impact of Bacterial Communities in Watermelon Seeds,” by Gillian E. Bergmann et al.—open access in Phytobiomes Journal: https://doi.org/10.1094/PBIOMES-08-25-0064-R

Fig. 3.
Genera shared between stigmas and seeds are generally abundant, with variation between tissues. A, We visualized the subset of bacterial communities that were shared between stigmas and seeds, aggregating to the top 20 most abundant genera in the subset. B, We then identified genera that are abundant in individual stigma and seed communities from the same parent plant. These plots were generated from 16S rRNA amplicon sequencing data.

Phytobiomes Journal @phytobiomesjournal.bsky.social · 3mo ago

Using shotgun metagenomic sequencing, Yunliang Li et al. examined the composition, function, and microbial association networks of root bacterial communities in two #Brassica napus genotypes with contrasting yields: https://doi.org/10.1094/PBIOMES-05-25-0033-R

Fig. 5.
Comparison of bacterial networks constructed using genera with differential association between NAM-23 and NAM-30. The similarities indicating the connection strength of two nodes are used as edge weights. Green edges correspond to positive estimated associations and red edges to negative ones. Node size is scaled by eigenvector centrality. The layout of both networks is the same.

Phytobiomes Journal @phytobiomesjournal.bsky.social · 3mo ago

Megan Teigen and Catalina Cuellar-Gempeler present functional insights on prey breakdown and nitrogen cycling from bacteria isolated from carnivorous plants. Learn more: https://doi.org/10.1094/PBIOMES-05-25-0039-R

Fig. 3.
Positive correlation between prey degradation and species richness in mixed culture. The dashed line indicates zero, and the solid line represents the linear regression model fitted to fly cage mass loss and species richness. The numbers 1 to 20 correspond to the bacterial group numbers in Table 2.

Phytobiomes Journal @phytobiomesjournal.bsky.social · 4mo ago

Short Communication: “Assessing the Effectiveness of Propidium Monoazide on the Viable Bacterial Microbiome in Huanglongbing-Affected Citrus via 16S rRNA Amplicon Sequencing,” by Chuanyu Yang et al. Learn more: https://doi.org/10.1094/PBIOMES-08-25-0059-SC

Fig. 1.
UniFrac-weighted principal coordinate analysis of propidium monoazide–treated (PMA+) huanglongbing-affected leaf samples in PMA treatment and non-PMA treatment at 0 days (0d), 15 days (15d), and 45 days (45d) after oxytetracycline (OTC) or water treatment. Analysis of similarities was performed to evaluate the significant differences in microbial community using QIIME (version 1.8.0) (P < 0.05). Red color indicates PMA treatment, and blue color indicates non-PMA treatment. Square indicates OTC treatment, and triangle indicates water treatment. PC1, principal coordinate 1; PC2, principal coordinate 2.

Phytobiomes Journal @phytobiomesjournal.bsky.social · 4mo ago

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.
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.

Phytobiomes Journal @phytobiomesjournal.bsky.social · 4mo ago

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.
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).

Phytobiomes Journal @phytobiomesjournal.bsky.social · 4mo ago

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. 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.

Phytobiomes Journal @phytobiomesjournal.bsky.social · 4mo ago

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. 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.

Phytobiomes Journal @phytobiomesjournal.bsky.social · 5mo ago

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. 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.

Phytobiomes Journal @phytobiomesjournal.bsky.social · 5mo ago

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.
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.

Phytobiomes Journal @phytobiomesjournal.bsky.social · 5mo ago

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.
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.

Phytobiomes Journal @phytobiomesjournal.bsky.social · 5mo ago

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.
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.

Phytobiomes Journal @phytobiomesjournal.bsky.social · 5mo ago

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

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.

Phytobiomes Journal @phytobiomesjournal.bsky.social · 6mo ago

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

A plant ‘vaccine’ takes on corn rootworm, a fearsome pest

Inoculating soil with pink microbes could help reduce the use of toxic insecticides.

science.org

Phytobiomes Journal @phytobiomesjournal.bsky.social · 6mo ago

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. 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.

Phytobiomes Journal @phytobiomesjournal.bsky.social · 6mo ago

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

Phytobiomes Journal @phytobiomesjournal.bsky.social · 6mo ago

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

Phytobiomes Journal @phytobiomesjournal.bsky.social · 7mo ago

“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.

Phytobiomes Journal @phytobiomesjournal.bsky.social · 7mo ago

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

Phytobiomes Journal @phytobiomesjournal.bsky.social · 7mo ago

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

Phytobiomes Journal @phytobiomesjournal.bsky.social · 7mo ago

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.

Phytobiomes Journal @phytobiomesjournal.bsky.social · 8mo ago

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.

Phytobiomes Journal @phytobiomesjournal.bsky.social · 8mo ago

“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.