Host specificity of plant-associated bacteria is negatively associated with genome size and host abundance along a latitudinal gradient.

Host specialization plays a critical role in the ecology and evolution of plant-microbe symbiosis. Theory predicts that host specialization is associated with microbial genome streamlining and is influenced by the abundance of host species, both of which can vary across latitudes, leading to a latitudinal gradient in host specificity. Here, we quantified the host specificity and composition of plant-bacteria symbioses on leaves across 329 tree species spanning a latitudinal gradient. Our analysis revealed a predominance of host-specialized leaf bacteria. The degree of host specificity was negatively correlated with bacterial genome size and the local abundance of host plants. Additionally, we found an increased host specificity at lower latitudes, aligning with the high prevalence of small bacterial genomes and rare host species in the tropics. These findings underscore the importance of genome streamlining and host abundance in the evolution of host specificity in plant-associated bacteria along the latitudinal gradient.

Climate mismatches with ectomycorrhizal fungi contribute to migration lag in North American tree range shifts.

Climate change will likely shift plant and microbial distributions, creating geographic mismatches between plant hosts and essential microbial symbionts (e.g., ectomycorrhizal fungi, EMF). The loss of historical interactions, or the gain of novel associations, can have important consequences for biodiversity, ecosystem processes, and plant migration potential, yet few analyses exist that measure where mycorrhizal symbioses could be lost or gained across landscapes. Here, we examine climate change impacts on tree-EMF codistributions at the continent scale. We built species distribution models for 400 EMF species and 50 tree species, integrating fungal sequencing data from North American forest ecosystems with tree species occurrence records and long-term forest inventory data. Our results show the following: 1) tree and EMF climate suitability to shift toward higher latitudes; 2) climate shifts increase the size of shared tree-EMF habitat overall, but 35% of tree-EMF pairs are at risk of declining habitat overlap; 3) climate mismatches between trees and EMF are projected to be greater at northern vs. southern boundaries; and 4) tree migration lag is correlated with lower richness of climatically suitable EMF partners. This work represents a concentrated effort to quantify the spatial extent and location of tree-EMF climate envelope mismatches. Our findings also support a biotic mechanism partially explaining the failure of northward tree species migrations with climate change: reduced diversity of co-occurring and climate-compatible EMF symbionts at higher latitudes. We highlight the conservation implications for identifying areas where tree and EMF responses to climate change may be highly divergent.

Development of transgenic Paulownia trees expressing antimicrobial thionin genes for enhanced resistance to fungal infections using chitosan nanoparticles.

There is an increasing focus on genetically altering Paulownia trees to enhance their resistance against fungal infections, given their rapid growth and quality wood production. The aim of this research was to establish a technique for incorporating two antimicrobial thionin genes, namely thionin-60 (thio-60) and thionin-63 (thio-63), into Paulownia tomentosa and Paulownia hybrid 9501 through the utilization of chitosan nanoparticles. The outcomes revealed the successful gene transfer into Paulownia trees utilizing chitosan nanoparticles. The effectiveness of thionin proteins against plant pathogens Fusarium and Aspergillus was examined, with a specific focus on Fusarium equiseti due to limited available data. In non-transgenic Paulownia species, the leaf weight inhibition percentage varied from 25 to 36 %, whereas in transgenic species, it ranged from 22 to 7 %. In general, Paulownia species expressing thio-60 displayed increased resistance to F. equiseti, while those expressing thio-63 exhibited heightened resistance to A. niger infection. The thionin proteins displayed a strong affinity for the phospholipid bilayer of the fungal cell membrane, demonstrating their capability to disrupt its structure. The transgenic plants created through this technique showed increased resistance to fungal infections. Thionin-60 demonstrated superior antifungal properties in comparison to thio-63, being more effective at disturbing the fungal cell membrane. These findings indicate that thio-60 holds potential as a novel antifungal agent and presents a promising approach for enhancing the antimicrobial traits of genetically modified Paulownia trees.

Influence of tree mycorrhizal type, tree species identity, and diversity on forest root-associated mycobiomes.

Understanding the complex interactions between trees and fungi is crucial for forest ecosystem management, yet the influence of tree mycorrhizal types, species identity, and diversity on tree-tree interactions and their root-associated fungal communities remains poorly understood. Our study addresses this gap by investigating root-associated fungal communities of different arbuscular mycorrhizal (AM) and ectomycorrhizal (EcM) tree species pairs (TSPs) in a subtropical tree diversity experiment, spanning monospecific, two-species, and multi-species mixtures, utilizing Illumina sequencing of the ITS2 region. The study reveals that tree mycorrhizal type significantly impacts the alpha diversity of root-associated fungi in monospecific stands. Meanwhile, tree species identity's influence is modulated by overall tree diversity. Tree-related variables and spatial distance emerged as major drivers of variations in fungal community composition. Notably, in multi-species mixtures, compositional differences between root fungal communities of AM and EcM trees diminish, indicating a convergence of fungal communities irrespective of mycorrhizal type. Interestingly, dual mycorrhizal fungal communities were observed in these multi-species mixtures. This research underscores the pivotal role of mycorrhizal partnerships and the interplay of biotic and abiotic factors in shaping root fungal communities, particularly in varied tree diversity settings, and its implications for effective forest management and biodiversity conservation.

Mycorrhizal type and tree diversity affect foliar elemental pools and stoichiometry.

Species-specific differences in nutrient acquisition strategies allow for complementary use of resources among plants in mixtures, which may be further shaped by mycorrhizal associations. However, empirical evidence of this potential role of mycorrhizae is scarce, particularly for tree communities. We investigated the impact of tree species richness and mycorrhizal types, arbuscular mycorrhizal fungi (AM) and ectomycorrhizal fungi (EM), on above- and belowground carbon (C), nitrogen (N), and phosphorus (P) dynamics. Soil and soil microbial biomass elemental dynamics showed weak responses to tree species richness and none to mycorrhizal type. However, foliar elemental concentrations, stoichiometry, and pools were significantly affected by both treatments. Tree species richness increased foliar C and P pools but not N pools. Additive partitioning analyses showed that net biodiversity effects of foliar C, N, P pools in EM tree communities were driven by selection effects, but in mixtures of both mycorrhizal types by complementarity effects. Furthermore, increased tree species richness reduced soil nitrate availability, over 2 yr. Our results indicate that positive effects of tree diversity on aboveground nutrient storage are mediated by complementary mycorrhizal strategies and highlight the importance of using mixtures composed of tree species with different types of mycorrhizae to achieve more multifunctional afforestation.

Forest management positively reshapes the phyllosphere bacterial community and improves community stability.

Research has shown that forest management can improve the post-drought growth and resilience of Qinghai spruce in the eastern Qilian Mountains, located on the northeastern Tibetan Plateau. However, the impact of such management on the tree-associated phyllosphere microbiome is not yet fully understood. This study provides new evidence of positive forest management effects on the phyllosphere microbiome after extreme drought, from the perspectives of community diversity, structure, network inference, keystone species, and assembly processes. In managed Qinghai spruce forest, the α-diversity of the phyllosphere bacterial communities increased, whereas the ß-diversity decreased. In addition, the phyllosphere bacterial community became more stable and resistant, yet less complex, following forest management. Keystone species inferred from a bacterial network also changed under forest management. Furthermore, forest management mediated changes in community assembly processes, intensifying the influence of determinacy, while diminishing that of stochasticity. These findings support the hypothesis that management can re-assemble the phyllosphere bacterial community, enhance community stability, and ultimately improve tree growth. Overall, the study highlights the importance of forest management on the phyllosphere microbiome and furnishes new insights into forest conservation from the perspective of managing microbial processes and effects.

The influence of tree genus, phylogeny, and richness on the specificity, rarity, and diversity of ectomycorrhizal fungi.

Partner specificity is a well-documented phenomenon in biotic interactions, yet the factors that determine specificity in plant-fungal associations remain largely unknown. By utilizing composite soil samples, we identified the predictors that drive partner specificity in both plants and fungi, with a particular focus on ectomycorrhizal associations. Fungal guilds exhibited significant differences in overall partner preference and avoidance, richness, and specificity to specific tree genera. The highest level of specificity was observed in root endophytic and ectomycorrhizal associations, while the lowest was found in arbuscular mycorrhizal associations. The majority of ectomycorrhizal fungal species showed a preference for one of their partner trees, primarily at the plant genus level. Specialist ectomycorrhizal fungi were dominant in belowground communities in terms of species richness and relative abundance. Moreover, all tree genera (and occasionally species) demonstrated a preference for certain fungal groups. Partner specificity was not related to the rarity of fungi or plants or environmental conditions, except for soil pH. Depending on the partner tree genus, specific fungi became more prevalent and relatively more abundant with increasing stand age, tree dominance, and soil pH conditions optimal for the partner tree genus. The richness of partner tree species and increased evenness of ectomycorrhizal fungi in multi-host communities enhanced the species richness of ectomycorrhizal fungi. However, it was primarily the partner-generalist fungi that contributed to the high diversity of ectomycorrhizal fungi in mixed forests.

Microbiome properties in the root nodules of Prosopis cineraria, a leguminous desert tree.

We conducted a comprehensive analysis of the total microbiome and transcriptionally active microbiome communities in the roots and root nodules of Prosopis cineraria, an important leguminous tree in arid regions of many Asian countries. Mature P. cineraria trees growing in the desert did not exhibit any detected root nodules. However, we observed root nodules on the roots of P. cineraria growing on a desert farm and on young plants growing in a growth chamber, when inoculated with rhizosphere soil, including with rhizosphere soil from near desert tree roots that had no nodules. Compared to nearby soil, non-nodulated roots were enriched with Actinobacteria (e.g., Actinophytocola sp.), whereas root nodules sampled from the desert farm and growth chamber had abundant Alphaproteobacteria (e.g., Ensifer sp.). These nodules yielded many microbes in addition to such nitrogen-fixing bacteria as Ensifer and Sinorhizobium species. Significant differences exist in the composition and abundance of microbial isolates between the nodule surface and the nodule endosphere. Shotgun metagenome analysis of nodule endospheres revealed that the root nodules comprised over 90% bacterial DNA, whereas metatranscriptome analysis showed that the plant produces vastly more transcripts than the microbes in these nodules. Control inoculations demonstrated that four out of six Rhizobium, Agrobacterium, or Ensifer isolates purified from P. cineraria nodules produced nodules in the roots of P. cineraria seedlings under greenhouse conditions. The best nodulation was achieved when seedlings were inoculated with a mixture of those bacterial strains. Though root nodulation could be achieved under water stress conditions, nodule number and nodule biomass increased with copious water availability. .IMPORTANCEMicrobial communities were investigated in roots and root nodules of Prosopis cineraria, a leguminous tree species in arid Asian regions that is responsible for exceptionally important contributions to soil fertility in these dramatically dry locations. Soil removed from regions near nodule-free roots on these mature plants contained an abundance of bacteria with the genetic ability to generate nodules and fix nitrogen but did not normally nodulate in their native rhizosphere environment, suggesting a very different co-evolved relationship than that observed for herbaceous legumes. The relative over-expression of the low-gene-density plant DNA compared to the bacterial DNA in the nodules was also unexpected, indicating a very powerful induction of host genetic contributions within the nodule. Finally, the water dependence of nodulation in inoculated seedlings suggested a possible link between early seedling growth (before a deep root system can be developed) and the early development of nitrogen-fixing capability.

Global field collection data confirm an affinity of brown rot fungi for coniferous habitats and substrates.

Unlike 'white rot' (WR) wood-decomposing fungi that remove lignin to access cellulosic sugars, 'brown rot' (BR) fungi selectively extract sugars and leave lignin behind. The relative frequency and distribution of these fungal types (decay modes) have not been thoroughly assessed at a global scale; thus, the fate of one-third of Earth's aboveground carbon, wood lignin, remains unclear. Using c. 1.5 million fungal sporocarp and c. 30 million tree records from publicly accessible databases, we mapped and compared decay mode and tree type (conifer vs angiosperm) distributions. Additionally, we mined fungal record metadata to assess substrate specificity per decay mode. The global average for BR fungi proportion (BR/(BR + WR records)) was 13% and geographic variation was positively correlated (R2 = 0.45) with conifer trees proportion (conifer/(conifer + angiosperm records)). Most BR species (61%) were conifer, rather than angiosperm (22%), specialists. The reverse was true for WR (conifer: 19%; angiosperm: 62%). Global BR proportion patterns were predicted with greater accuracy using the relative distributions of individual tree species (R2 = 0.82), rather than tree type. Fungal decay mode distributions can be explained by tree type and, more importantly, tree species distributions, which our data suggest is due to strong substrate specificities.

Fungal community composition predicts forest carbon storage at a continental scale.

Forest soils harbor hyper-diverse microbial communities which fundamentally regulate carbon and nutrient cycling across the globe. Directly testing hypotheses on how microbiome diversity is linked to forest carbon storage has been difficult, due to a lack of paired data on microbiome diversity and in situ observations of forest carbon accumulation and storage. Here, we investigated the relationship between soil microbiomes and forest carbon across 238 forest inventory plots spanning 15 European countries. We show that the composition and diversity of fungal, but not bacterial, species is tightly coupled to both forest biotic conditions and a seven-fold variation in tree growth rates and biomass carbon stocks when controlling for the effects of dominant tree type, climate, and other environmental factors. This linkage is particularly strong for symbiotic endophytic and ectomycorrhizal fungi known to directly facilitate tree growth. Since tree growth rates in this system are closely and positively correlated with belowground soil carbon stocks, we conclude that fungal composition is a strong predictor of overall forest carbon storage across the European continent.

Ectomycorrhizal fungal communities in natural and urban ecosystems: Quercus humboldtii as a study case in the tropical Andes.

Worldwide urban landscapes are expanding because of the growing human population. Urban ecosystems serve as habitats to highly diverse communities. However, studies focusing on the diversity and structure of ectomycorrhizal communities are uncommon in this habitat. In Colombia, Quercus humboldtii Bonpl. is an ectomycorrhizal tree thriving in tropical montane forests hosting a high diversity of ectomycorrhizal fungi. Q. humboldtii is planted as an urban tree in Bogotá (Colombia). We studied how root-associated fungal communities of this tree change between natural and urban areas. Using Illumina sequencing, we amplified the ITS1 region and analyzed the resulting data using both OTUs and Amplicon Sequence Variants (ASVs) bioinformatics pipelines. The results obtained using both pipelines showed no substantial differences between OTUs and ASVs for the community patterns of root-associated fungi, and only differences in species richness were observed. We found no significant differences in the species richness between urban and rural sites based on Fisher's alpha or species-accumulation curves. However, we found significant differences in the community composition of fungi present in the roots of rural and urban trees with rural communities being dominated by Russula and Lactarius and urban communities by Scleroderma, Hydnangium, and Trechispora, suggesting a high impact of urban disturbances on ectomycorrhizal fungal communities. Our results highlight the importance of urban trees as reservoirs of fungal diversity and the potential impact of urban conditions on favoring fungal species adapted to more disturbed ecosystems.

Interplay of biotic and abiotic factors shapes tree seedling growth and root-associated microbial communities.

Root-associated microbes can alleviate plant abiotic stresses, thus potentially supporting adaptation to a changing climate or to novel environments during range expansion. While climate change is extending plant species fundamental niches northward, the distribution and colonization of mutualists (e.g., arbuscular mycorrhizal fungi) and pathogens may constrain plant growth and regeneration. Yet, the degree to which biotic and abiotic factors impact plant performance and associated microbial communities at the edge of their distribution remains unclear. Here, we use root microscopy, coupled with amplicon sequencing, to study bacterial, fungal, and mycorrhizal root-associated microbial communities from sugar maple seedlings distributed across two temperate-to-boreal elevational gradients in southern Québec, Canada. Our findings demonstrate that soil pH, soil Ca, and distance to sugar maple trees are key drivers of root-associated microbial communities, overshadowing the influence of elevation. Interestingly, changes in root fungal community composition mediate an indirect effect of soil pH on seedling growth, a pattern consistent at both sites. Overall, our findings highlight a complex role of biotic and abiotic factors in shaping tree-microbe interactions, which are in turn correlated with seedling growth. These findings have important ramifications for tree range expansion in response to shifting climatic niches.

Austropuccinia licaniae, first congeneric with the myrtle rust pathogen A. psidii.

In 1895 and 2001, rust fungi affecting Licania trees (Chrysobalanchaceae) in Brazil were described as Uredo licaniae by Hennings in the state of Goiás and as Phakopsora tomentosae by Ferreira et al. in the state of Amazonas, respectively. Recently, a Licania rust fungus collected close to the Amazonian type location sharing symptoms with the former two species was subjected to morphological examinations and molecular phylogenetic analyses using 28S nuc rDNA (ITS2-28S) and cytochrome c oxidase subunit III (CO3) gene sequences. Since the original type specimen of Ph. tomentosae is considered lost, we carefully reviewed the type description and questioned the identity of the telium, which justified the description of the fungus as a Phakopsora species. Furthermore, the additional revision of the type material described by Hennings revealed that Ph. tomentosae is a synonym of U. licaniae. Based on the morphological examinations, disease symptoms, and shared hosts, we concluded that the newly collected material is conspecific with U. licaniae. However, the phylogenetic analyses rejected allocation in Phakopsora and instead assigned the Licania rust fungus in a sister relationship with Austropuccinia psidii (Sphaerophragmiaceae), the causal agent of the globally invasive myrtle rust pathogen. We therefore favored a recombination of U. licaniae (syn. Ph. tomentosae) into Austropuccinia and proposed the new name Austropuccina licaniae for the second species now identified for this genus. The fungus shares conspicuous symptoms with A. psidii, causing often severe infections of growing leaves and shoots that lead to leaf necrosis, leaf shedding, and eventually to the dieback of entire shoots. In view of the very similar symptoms of its aggressively invasive sister species, we briefly discuss the current state of knowledge about A. licaniae and the potential risks, and the opportunity of its identification.

From individual leaves to forest stands: importance of niche, distance decay, and stochasticity vary by ecosystem type and functional group for fungal community composition.

Community assembly is influenced by environmental niche processes as well as stochastic processes that can be spatially dependent (e.g. dispersal limitation) or independent (e.g. priority effects). Here, we sampled senesced tree leaves as unit habitats to investigate fungal community assembly at two spatial scales: (i) small neighborhoods of overlapping leaves from differing tree species and (ii) forest stands of differing ecosystem types. Among forest stands, ecosystem type explained the most variation in community composition. Among adjacent leaves within stands, variability in fungal composition was surprisingly high. Leaf type was more important in stands with high soil fertility and dominated by differing tree mycorrhizal types (sugar maple vs. basswood or red oak), whereas distance decay was more important in oak-dominated forest stands with low soil fertility. Abundance of functional groups was explained by environmental factors, but predictors of taxonomic composition within differing functional groups were highly variable. These results suggest that fungal community assembly processes are clearest for functional group abundances and large spatial scales. Understanding fungal community assembly at smaller spatial scales will benefit from further study focusing on differences in drivers for different ecosystems and functional groups, as well as the importance of spatially independent factors such as priority effects.

Soil microbial community response to ectomycorrhizal dominance in diverse neotropical montane forests.

Ectomycorrhizal (EM) associations can promote the dominance of tree species in otherwise diverse tropical forests. These EM associations between trees and their fungal mutualists have important consequences for soil organic matter cycling, yet the influence of these EM-associated effects on surrounding microbial communities is not well known, particularly in neotropical forests. We examined fungal and prokaryotic community composition in surface soil samples from mixed arbuscular mycorrhizal (AM) and ectomycorrhizal (EM) stands as well as stands dominated by EM-associated Oreomunnea mexicana (Juglandaceae) in four watersheds differing in soil fertility in the Fortuna Forest Reserve, Panama. We hypothesized that EM-dominated stands would support distinct microbial community assemblages relative to the mixed AM-EM stands due to differences in carbon and nitrogen cycling associated with the dominance of EM trees. We expected that this microbiome selection in EM-dominated stands would lead to lower overall microbial community diversity and turnover, with tighter correspondence between general fungal and prokaryotic communities. We measured fungal and prokaryotic community composition via high-throughput Illumina sequencing of the ITS2 (fungi) and 16S rRNA (prokaryotic) gene regions. We analyzed differences in alpha and beta diversity between forest stands associated with different mycorrhizal types, as well as the relative abundance of fungal functional groups and various microbial taxa. We found that fungal and prokaryotic community composition differed based on stand mycorrhizal type. There was lower prokaryotic diversity and lower relative abundance of fungal saprotrophs and pathogens in EM-dominated than AM-EM mixed stands. However, contrary to our prediction, there was lower homogeneity for fungal communities in EM-dominated stands compared to mixed AM-EM stands. Overall, we demonstrate that EM-dominated tropical forest stands have distinct soil microbiomes relative to surrounding diverse forests, suggesting that EM fungi may filter microbial functional groups in ways that could potentially influence plant performance or ecosystem function.

Aboveground plants determine the exchange of pathogens within air-phyllosphere-soil continuum in urban greenspaces.

The microbiome in the air-phyllosphere-soil continuum of urban greenspaces plays a crucial role in re-connecting urban populations with biodiverse environmental microbiomes. However, little is known about whether plant type affects the airborne microbiomes, as well as the extent to which soil and phyllosphere microbiomes contribute to airborne microbiomes. Here we collected soil, phyllosphere and airborne microbes with different plant types (broadleaf tree, conifer tree, and grass) in urban parks. Despite the significant impacts of plant type on soil and phyllosphere microbiomes, plant type had no obvious effects on the diversity of airborne microbes but shaped airborne bacterial composition in urban greenspaces. Soil and phyllosphere microbiomes had a higher contribution to airborne bacteria in broadleaf trees (37.56%) compared to conifer trees (9.51%) and grasses (14.29%). Grass areas in urban greenspaces exhibited a greater proportion of potential pathogens compared to the tree areas. The abundance of bacterial pathogens in phyllosphere was significantly higher in grasses compared to broadleaf and conifer trees. Together, our study provides novel insights into the microbiome patterns in air-phyllosphere-soil continuum, highlighting the potential significance of reducing the proportion of extensively human-intervened grass areas in future urban environment designs to enhance the provision of ecosystem services in urban greenspaces.

Shifts in bacterial traits under chronic nitrogen deposition align with soil processes in arbuscular, but not ectomycorrhizal-associated trees.

Nitrogen (N) deposition increases soil carbon (C) storage by reducing microbial activity. These effects vary in soil beneath trees that associate with arbuscular (AM) and ectomycorrhizal (ECM) fungi. Variation in carbon C and N uptake traits among microbes may explain differences in soil nutrient cycling between mycorrhizal associations in response to high N loads, a mechanism not previously examined due to methodological limitations. Here, we used quantitative Stable Isotope Probing (qSIP) to measure bacterial C and N assimilation rates from an added organic compound, which we conceptualize as functional traits. As such, we applied a trait-based approach to explore whether variation in assimilation rates of bacterial taxa can inform shifts in soil function under chronic N deposition. We show taxon-specific and community-wide declines of bacterial C and N uptake under chronic N deposition in both AM and ECM soils. N deposition-induced reductions in microbial activity were mirrored by declines in soil organic matter mineralization rates in AM but not ECM soils. Our findings suggest C and N uptake traits of bacterial communities can predict C cycling feedbacks to N deposition in AM soils, but additional data, for instance on the traits of fungi, may be needed to connect microbial traits with soil C and N cycling in ECM systems. Our study also highlights the potential of employing qSIP in conjunction with trait-based analytical approaches to inform how ecological processes of microbial communities influence soil functioning.

Mapping bark bacteria: initial insights of stemflow-induced changes in bark surface phyla.

IMPORTANCE: Compared with the phyllosphere, bacteria inhabiting bark surfaces are inadequately understood. Based on a preliminary pilot study, our work suggests that microbial populations vary across tree bark surfaces and may differ in relation to surrounding land use. Initial results suggest that stemflow, the water that flows along the bark surface, actively moves bacterial communities across a tree. These preliminary findings underscore the need for further study of niche microbial populations to determine whether there are connections between the biodiversity of microbiomes inhabiting corticular surfaces, land use, and hydrology.

Above- and belowground fungal biodiversity of Populus trees on a continental scale.

Understanding drivers of terrestrial fungal communities over large scales is an important challenge for predicting the fate of ecosystems under climate change and providing critical ecological context for bioengineering plant-microbe interactions in model systems. We conducted an extensive molecular and microscopy field study across the contiguous United States measuring natural variation in the Populus fungal microbiome among tree species, plant niche compartments and key symbionts. Our results show clear biodiversity hotspots and regional endemism of Populus-associated fungal communities explained by a combination of climate, soil and geographic factors. Modelling climate change impacts showed a deterioration of Populus mycorrhizal associations and an increase in potentially pathogenic foliar endophyte diversity and prevalence. Geographic differences among these symbiont groups in their sensitivity to environmental change are likely to influence broader forest health and ecosystem function. This dataset provides an above- and belowground atlas of Populus fungal biodiversity at a continental scale.

Visualization of root extracellular traps in an ectomycorrhizal woody plant (Pinus densiflora) and their interactions with root-associated bacteria.

MAIN CONCLUSION: Extracellular traps in the primary root of Pinus densiflora contribute to root-associated bacterial colonization. Trapped rhizobacteria induce the production of reactive oxygen species in root-associated, cap-derived cells. Ectomycorrhizal (ECM) woody plants, such as members of Pinaceae and Fagaceae, can acquire resistance to biotic and abiotic stresses through the formation of mycorrhiza with ECM fungi. However, germinated tree seedlings do not have mycorrhizae and it takes several weeks for ectomycorrhizae to form on their root tips. Therefore, to confer protection during the early growth stage, bare primary roots require defense mechanisms other than mycorrhization. Here, we attempted to visualize root extracellular traps (RETs), an innate root defense mechanism, in the primary root of Pinus densiflora and investigate the interactions with root-associated bacteria isolated from ECM and fine non-mycorrhizal roots. Histological and histochemical imaging and colony-forming unit assays demonstrated that RETs in P. densiflora, mainly consisting of root-associated, cap-derived cells (AC-DCs) and large amounts of root mucilage, promote bacterial colonization in the rhizosphere, despite also having bactericidal activity via extracellular DNA. Four rhizobacterial strains retarded the mycelial growth of a pathogenic strain belonging to the Fusarium oxysporum species complex in dual culture assay. They also induced the production of reactive oxygen species (ROS) from host tree AC-DCs without being excluded from the rhizosphere of P. densiflora. Applying three Paraburkholderia strains, especially PM O-EM8 and PF T-NM22, showed significant differences in the ROS levels from the control group. These results reveal the indirect contributions of rhizobacteria to host root defense and suggest that root-associated bacteria could be a component of RETs as a first line of defense against root pathogens in the early growth stage of ECM woody plants.