Assembly of the Populus Microbiome Is Temporally Dynamic and Determined by Selective and Stochastic Factors

Amplicon sequencing and culture-dependent approaches reveal core bacterial endophytes aiding freezing stress tolerance in alpine Rosaceae plants

Wild plants growing in alpine regions are associated with endophytic microbial communities that may support plant growth and survival under cold conditions. The structure and function of endophytic bacterial communities were characterized in flowers, leaves, and roots of three alpine Rosaceae plants in Alpine areas using a combined amplicon sequencing and culture-dependent approaches to determine the role of core taxa on plant freezing stress tolerance. Amplicon sequencing analysis revealed that plant tissue, collection site, and host plant are the main factors affecting the richness, diversity, and taxonomic structure of endophytic bacterial communities in alpine Rosaceae plants. Core endophytic bacterial taxa were identified as 31 amplicon sequence variants highly prevalent across all plant tissues. Psychrotolerant bacterial endophytes belonging to the core taxa of Duganella, Erwinia, Pseudomonas, and Rhizobium genera mitigated freezing stress in strawberry plants, demonstrating the beneficial role of endophytic bacterial communities and their potential use for cold stress mitigation in agriculture.IMPORTANCEFreezing stress is one of the major abiotic stresses affecting fruit production in Rosaceae crops. Current strategies to reduce freezing damage include physical and chemical methods, which have several limitations in terms of costs, efficacy, feasibility, and environmental impacts. The use or manipulation of plant-associated microbial communities was proposed as a promising sustainable approach to alleviate cold stress in crops, but no information is available on the possible mitigation of freezing stress in Rosaceae plants. A combination of amplicon sequencing, culture-dependent, and plant bioassay approaches revealed the beneficial role of the endophytic bacterial communities in alpine Rosaceae plants. In particular, we showed that culturable psychrotolerant bacterial endophytes belonging to the core taxa of Duganella, Erwinia, Pseudomonas, and Rhizobium genera can mitigate freezing stress on strawberry seedlings. Overall, this study demonstrates the potential use of psychrotolerant bacterial endophytes for the development of biostimulants for cold stress mitigation in agriculture.

Dynamic soil columns simulate Arctic redox biogeochemistry and carbon release during changes in water saturation

Thawing Arctic permafrost can induce hydrologic change and alter redox conditions, shifting the balance of soil organic matter (SOM) decomposition. There remains uncertainty about how soil saturation and redox transitions impact dissolved and gas phase carbon fluxes, and efforts to link hydrobiogeochemical processes to ecosystem-scale models are limited. This study evaluates SOM decomposition of Arctic tundra soils using column experiments, water chemistry measurements, microbial community analysis, and a PFLOTRAN reactive transport model. Soil columns from a thermokarst channel (TC) and an upland tundra (UC) were exposed to cycles of saturation and drainage, which controlled carbon emissions. During saturation, an outflow of dissolved organic carbon from the UC soil correlated with elevated reduced iron and decreased pH; during drainage, UC carbon dioxide fluxes were 70% higher than TC fluxes. Intermittent methane release was observed for TC, consistent with higher methanogen abundance. Slower drainage in the TC soil correlated with more subtle biogeochemical changes. PFLOTRAN simulations captured experimental trends in soil carbon fluxes, oxygen concentrations, and water contents. The model was then used to evaluate additional soil water drainage rates. This study emphasizes the importance of considering hydrologic change when evaluating and simulating SOM decomposition in dynamic Arctic tundra environments.

Catabolic pathway acquisition by rhizosphere bacteria readily enables growth with a root exudate component but does not affect root colonization

Horizontal gene transfer (HGT) is a fundamental evolutionary process that plays a key role in bacterial evolution. The likelihood of a successful transfer event is expected to depend on the precise balance of costs and benefits resulting from pathway acquisition. Most experimental analyses of HGT have focused on phenotypes that have large fitness benefits under appropriate selective conditions, such as antibiotic resistance. However, many examples of HGT involve phenotypes that are predicted to provide smaller benefits, such as the ability to catabolize additional carbon sources. We have experimentally simulated the consequences of one such HGT event in the laboratory, studying the effects of transferring a pathway for catabolism of the plant-derived aromatic compound salicyl alcohol between rhizosphere isolates from the Pseudomonas genus. We find that pathway acquisition enables rapid catabolism of salicyl alcohol with only minor disruptions to the existing metabolic and regulatory networks of the new host. However, this new catabolic potential does not confer a measurable fitness advantage during competitive growth in the rhizosphere. We conclude that the phenotype of salicyl alcohol catabolism is readily transferable but is selectively neutral under environmentally relevant conditions. We propose that this condition is common and that HGT of many pathways will be self-limiting because the selective benefits are small.IMPORTANCEHorizontal gene transfer (HGT) is a key process in microbial evolution, but the factors limiting HGT are poorly understood. Aside from the rather unique scenario of antibiotic resistance, the evolutionary benefits of pathway acquisition are still unclear. To experimentally test the effects of pathway acquisition, we transferred a pathway for catabolism of a plant-derived aromatic compound between soil bacteria isolated from the roots of poplar trees and determined the resulting phenotypic and fitness effects. We found that pathway acquisition allowed bacteria to grow using the plant-derived compound in the laboratory, but that this new phenotype did not provide an advantage when the bacteria were reinoculated onto plant roots. These results suggest that the benefits of pathway acquisition may be small when measured under ecologically-relevant conditions. From an engineering perspective, efforts to alter microbial community composition in situ by manipulating catabolic pathways or nutrient availability will be challenging when gaining access to a new niche does not provide a benefit.

Investigating Microbial Diversity in the Endosphere and Rhizoplane of Three Aromatic Rice Landraces: Implications for Biological Nitrogen Fixation

Biological nitrogen fixation (BNF) occurring in the rhizosphere is a sustainable source of nitrogen for plants. BNF in cereal crops can be promoted by inoculation of a single or consortium of associative and endophytic diazotrophs. Creating a successful nitrogen-fixing biofertilizer necessitates the study of the core microbiome of the plant rhizosphere and the functional relationship of the members. This study compares the endosphere and rhizoplane microbial diversity of three aromatic landraces and one high-yielding variety of rice using culture-independent methods. The V3-V4 variable regions of 16S rRNA were used for amplicon sequencing of soil DNA. Patescibacteria, Planctomycetota, and Proteobacteria were the predominant phyla in all four genotypes. Richness (Chao-1 and ACE) and microbial diversity indices (Shannon and Simpson indices) showed that microbial diversity among the genotypes varies subtly at the phylum level. Beta diversity analysis with the phylum identified and comparisons of the microbiome at the genus level revealed a more prominent effect of plant genotype on microbial diversity. Canonical component analysis drew a correlation between microbial diversity in each genotype with the sugar and N content of these landraces. Paraburkholderia was identified as one of the major OTUs among the known nitrogen fixing followed by Allorhizobium-Neorhizobium-Pararhizobium-Rhizobium group, Azospirillum, Hebarspirillum, and Azotobacter.

Microbial colonisation rewires the composition and content of poplar root exudates, root and shoot metabolomes

BACKGROUND

Trees are associated with a broad range of microorganisms colonising the diverse tissues of their host. However, the early dynamics of the microbiota assembly microbiota from the root to shoot axis and how it is linked to root exudates and metabolite contents of tissues remain unclear. Here, we characterised how fungal and bacterial communities are altering root exudates as well as root and shoot metabolomes in parallel with their establishment in poplar cuttings (Populus tremula x tremuloides clone T89) over 30 days of growth. Sterile poplar cuttings were planted in natural or gamma irradiated soils. Bulk and rhizospheric soils, root and shoot tissues were collected from day 1 to day 30 to track the dynamic changes of fungal and bacterial communities in the different habitats by DNA metabarcoding. Root exudates and root and shoot metabolites were analysed in parallel by gas chromatography-mass spectrometry.

RESULTS

Our study reveals that microbial colonisation triggered rapid and substantial alterations in both the composition and quantity of root exudates, with over 70 metabolites exclusively identified in remarkably high abundances in the absence of microorganisms. Noteworthy among these were lipid-related metabolites and defence compounds. The microbial colonisation of both roots and shoots exhibited a similar dynamic response, initially involving saprophytic microorganisms and later transitioning to endophytes and symbionts. Key constituents of the shoot microbiota were also discernible at earlier time points in the rhizosphere and roots, indicating that the soil constituted a primary source for shoot microbiota. Furthermore, the microbial colonisation of belowground and aerial compartments induced a reconfiguration of plant metabolism. Specifically, microbial colonisation predominantly instigated alterations in primary metabolism in roots, while in shoots, it primarily influenced defence metabolism.

CONCLUSIONS

This study highlighted the profound impact of microbial interactions on metabolic pathways of plants, shedding light on the intricate interplay between plants and their associated microbial communities. Video Abstract.

Stochastic processes drive the dynamic assembly of bacterial communities in Salix matsudana afforested soils

Introduction

This study investigates the dynamic shifts in soil bacterial communities within a Salix matsudana afforested ecosystem transitioning from agricultural land. Understanding the temporal variability in bacterial diversity and community structures is crucial for informing forest management and conservation strategies, particularly in regions undergoing afforestation.

Methods

We employed high-throughput sequencing across three distinct months (August, September, and October) to analyze the temporal variability in bacterial community composition and diversity. Network analysis was utilized to identify keystone species and assess community stability under varying environmental conditions, including fluctuations in temperature and precipitation.

Results

We uncover significant temporal variability in bacterial diversity and community structures, which are closely tied to fluctuations in temperature and precipitation. Our findings reveal the abundance of the dominant bacterial phyla, such as Actinobacteria and Proteobacteria, which did not change overall, highlighting the stability and resilience of the microbial community across seasonal transitions. Notably, the increasing similarity in community composition from August to October indicates a reduction in species turnover, likely driven by more homogeneous environmental conditions. Through comprehensive network analysis, we identify the pivotal role of keystone species, particularly the human pathogen Nocardia, in maintaining community stability under reduced soil moisture. The observed variations in community connectivity underscore the microbial community's resilience and adaptability to seasonal shifts, with higher stability in August and October contrasting with the instability observed in September.

Discussion

These results underscore the complex interplay between stochastic and deterministic processes in bacterial community assembly, significantly shaped by prevailing environmental conditions. The insights gained from this research have far-reaching implications for forestry management and conservation strategies, particularly in regions undergoing similar afforestation efforts.

Enrichment of novel entomopathogenic Pseudomonas species enhances willow resistance to leaf beetles

BACKGROUND

Plants have evolved various defense mechanisms against insect herbivores, including the formation of physical barriers, the synthesis of toxic metabolites, and the activation of phytohormone responses. Although plant-associated microbiota influence plant growth and health, whether they play a role in plant defense against insect pests in natural ecosystems is unknown.

RESULTS

Here, we show that leaves of beetle-damaged weeping willow (Salix babylonica) trees are more resistant to the leaf beetle Plagiodera versicolora (Coleoptera) than those of undamaged leaves. Bacterial community transplantation experiments demonstrated that plant-associated microbiota from the beetle-damaged willow contribute to the resistance of the beetle-damaged willow to P. versicolora. Analysis of the composition and abundance of the microbiome revealed that Pseudomonas spp. is significantly enriched in the phyllosphere, roots, and rhizosphere soil of beetle-damaged willows relative to undamaged willows. From a total of 49 Pseudomonas strains isolated from willows and rhizosphere soil, we identified seven novel Pseudomonas strains that are toxic to P. versicolora. Moreover, re-inoculation of a synthetic microbial community (SynCom) with these Pseudomonas strains enhances willow resistance to P. versicolora.

CONCLUSIONS

Collectively, our data reveal that willows can exploit specific entomopathogenic bacteria to enhance defense against P. versicolora, suggesting that there is a complex interplay among plants, insects, and plant-associated microbiota in natural ecosystems.

Unveiling the influence of salinity on bacterial microbiome assembly of halophytes and crops

BACKGROUND

Climate change and anthropogenic activities intensify salinity stress impacting significantly on plant productivity and biodiversity in agroecosystems. There are naturally salt-tolerant plants (halophytes) that can grow and withstand such harsh conditions. Halophytes have evolved along with their associated microbiota to adapt to hypersaline environments. Identifying shared microbial taxa between halophyte species has rarely been investigated. We performed a comprehensive meta-analysis using the published bacterial 16S rRNA gene sequence datasets to untangle the rhizosphere microbiota structure of two halophyte groups and non-halophytes. We aimed for the identification of marker taxa of plants being adapted to a high salinity using three independent approaches.

RESULTS

Fifteen studies met the selection criteria for downstream analysis, consisting of 40 plants representing diverse halophyte and non-halophyte species. Microbiome structural analysis revealed distinct compositions for halophytes that face high salt concentrations in their rhizosphere compared to halophytes grown at low salt concentrations or from non-halophytes. For halophytes grown at high salt concentrations, we discovered three bacterial genera that were independently detected through the analysis of the core microbiome, key hub taxa by network analysis and random forest analysis. These genera were Thalassospira, Erythrobacter, and Marinobacter.

CONCLUSIONS

Our meta-analysis revealed that salinity level is a critical factor in affecting the rhizosphere microbiome assembly of plants. Detecting marker taxa across high-halophytes may help to select Bacteria that might improve the salt tolerance of non-halophytic plants.

Genetic architecture of heritable leaf microbes

Host-associated microbiomes are shaped by both their environment and host genetics, and often impact host performance. The scale of host genetic variation important to microbes is largely unknown yet fundamental to the community assembly of host-associated microbiomes, with implications for the eco-evolutionary dynamics of microbes and hosts. Using Ipomoea hederacea, ivyleaf morning glory, we generated matrilines differing in quantitative genetic variation and leaf shape, which is controlled by a single Mendelian locus. We then investigated the relative roles of Mendelian and quantitative genetic variation in structuring the leaf microbiome and how these two sources of genetic variation contributed to microbe heritability. We found that despite large effects of the environment, both Mendelian and quantitative genetic host variation contribute to microbe heritability and that the cumulative small effect genomic differences due to matriline explained as much or more microbial variation than a single large effect Mendelian locus. Furthermore, our results are the first to suggest that leaf shape itself contributes to variation in the abundances of some phyllosphere microbes.IMPORTANCEWe investigated how host genetic variation affects the assembly of Ipomoea hederacea's natural microbiome. We found that the genetic architecture of leaf-associated microbiomes involves both quantitative genetic variation and Mendelian traits, with similar contributions to microbe heritability. The existence of Mendelian and quantitative genetic variation for host-associated microbes means that plant evolution at the leaf shape locus or other quantitative genetic loci has the potential to shape microbial abundance and community composition.

Seasonality and longer-term development generate temporal dynamics in the Populus microbiome

Temporal variation in community composition is central to our understanding of the assembly and functioning of microbial communities, yet the controls over temporal dynamics for microbiomes of long-lived plants, such as trees, remain unclear. Temporal variation in tree microbiomes could arise primarily from seasonal (i.e., intra-annual) fluctuations in community composition or from longer-term changes across years as host plants age. To test these alternatives, we experimentally isolated temporal variation in plant microbiome composition using a common garden and clonally propagated plants, and we used amplicon sequencing to characterize bacterial/archaeal and fungal communities in the leaf endosphere, root endosphere, and rhizosphere of two Populus spp. over four seasons across two consecutive years. Microbial community composition differed among seasons and years (which accounted for up to 21% of the variation in microbial community composition) and was correlated with seasonal dissimilarity in climatic conditions. However, microbial community dissimilarity was also positively correlated with time, reflecting longer-term compositional shifts as host trees aged. Together, our findings demonstrate that temporal patterns in tree microbiomes arise from both seasonal fluctuations and longer-term changes, which interact to generate unique seasonal patterns each year. In addition to shedding light on two important controls over the assembly of plant microbiomes, our results also suggest future studies of tree microbiomes should account for background temporal dynamics when testing the drivers of spatial patterns in microbial community composition and temporal responses of plant microbiomes to environmental change.IMPORTANCEMicrobiomes are integral to the health of host plants, but we have a limited understanding of the factors that control how the composition of plant microbiomes changes over time. Especially little is known about the microbiome of long-lived trees, relative to annual and non-woody plants. We tested how tree microbiomes changed between seasons and years in poplar (genus Populus), which are widespread and ecologically important tree species that also serve as important biofuel feedstocks. We found the composition of bacterial, archaeal, and fungal communities differed among seasons, but these seasonal differences depended on year. This dependence was driven by longer-term changes in microbial composition as host trees developed across consecutive years. Our findings suggest that temporal variation in tree microbiomes is driven by both seasonal fluctuations and longer-term (i.e., multiyear) development.

Assemblages of rhizospheric and root endospheric mycobiota and their ecological associations with functional traits of rice

The soil-root interface harbors complex fungal communities that play vital roles in the fitness of host plants. However, little is known about the assembly rules and potential functions of rhizospheric and endospheric mycobiota. A greenhouse experiment was conducted to explore the fungal communities inhabiting the rhizosphere and roots of 87 rice cultivars at the tillering stage via amplicon sequencing of the fungal internal transcribed spacer 1 region. The potential relationships between these communities and host plant functional traits were also investigated using Procrustes analysis, generalized additive model fitting, and correlation analysis. The fungal microbiota exhibited greater richness, higher diversity, and lower structural variability in the rhizosphere than in the root endosphere. Compared with the root endosphere, the rhizosphere supported a larger coabundance network, with greater connectivity and stronger cohesion. Null model-based analyses revealed that dispersal limitation was primarily responsible for rhizosphere fungal community assembly, while ecological drift was the dominant process in the root endosphere. The community composition of fungi in the rhizosphere was shown to be more related to plant functional traits, such as the root/whole plant biomass, root:shoot biomass ratio, root/shoot nitrogen (N) content, and root/shoot/whole plant N accumulation, than to that in the root endosphere. Overall, at the early stage of rice growth, diverse and complex rhizospheric fungal communities are shaped by stochastic-based processes and exhibit stronger associations with plant functional traits.

IMPORTANCE

The assembly processes and functions of root-associated mycobiota are among the most fascinating yet elusive topics in microbial ecology. Our results revealed that stochastic forces (dispersal limitation or ecological drift) act on fungal community assembly in both the rice rhizosphere and root endosphere at the early stage of plant growth. In addition, high covariations between the rhizosphere fungal community compositions and plant functional trait profiles were clearly demonstrated in the present study. This work provides empirical evidence of the root-associated fungal assembly principles and ecological relationships of plant functional traits with rhizospheric and root endospheric mycobiota, thereby potentially providing novel perspectives for enhancing plant performance.

Temporal assembly patterns of microbial communities in three parallel bioreactors treating low-concentration coking wastewater with differing carbon source concentrations

Carbon source is an important factor of biological treatment systems, the effects of which on their temporal community assembly patterns are not sufficiently understood currently. In this study, the temporal dynamics and driving mechanisms of the communities in three parallel bioreactors for low-concentration coking wastewater (CWW) treatment with differing carbon source concentrations (S0 with no glucose addition, S1 with 200 mg/L glucose addition and S2 with 400 mg/L glucose addition) were comprehensively studied. High-throughput sequencing and bioinformatics analyses including network analysis and Infer Community Assembly Mechanisms by Phylogenetic bin-based null model (iCAMP) were used. The communities of three systems showed turnover rates of 0.0029∼0.0034 every 15 days. Network analysis results showed that the S0 network showed higher positive correlation proportion (71.43%) and clustering coefficient (0.33), suggesting that carbon source shortage in S0 promoted interactions and cooperation of microbes. The neutral community model analysis showed that the immigration rate increased from 0.5247 in S0 to 0.6478 in S2. The iCAMP analysis results showed that drift (45.89%) and homogeneous selection (31.68%) dominated in driving the assembly of all the investigated microbial communities. The contribution of homogeneous selection increased with the increase of carbon source concentrations, from 27.92% in S0 to 36.08% in S2. The OTUs participating in aerobic respiration and tricarboxylic acid (TCA) cycle were abundant among the bins mainly affected by deterministic processes, while those related to the metabolism of refractory organic pollutants in CWW such as alkanes, benzenes and phenols were abundant in the bins dominated by stochastic processes.

Scrutinizing microbiome determinism: why deterministic hypotheses about the microbiome are conceptually ungrounded

This paper addresses the topic of determinism in contemporary microbiome research. I distinguish two types of deterministic claims about the microbiome, and I show evidence that both types of claims are present in the contemporary literature. First, the idea that the host genetics determines the composition of the microbiome which I call "host-microbiome determinism". Second, the idea that the genetics of the holobiont (the individual unit composed by a host plus its microbiome) determines the expression of certain phenotypic traits, which I call "microbiome-phenotype determinism". Drawing on the stability of traits conception of individuality (Suárez in Hist Philos Life Sci 42:11, 2020) I argue that none of these deterministic hypotheses is grounded on our current knowledge of how the holobiont is transgenerationally assembled, nor how it expresses its phenotypic traits.

Editing Metabolism, Sex, and Microbiome: How Can We Help Poplar Resist Pathogens?

Poplar (Populus) is a genus of woody plants of great economic value. Due to the growing economic importance of poplar, there is a need to ensure its stable growth by increasing its resistance to pathogens. Genetic engineering can create organisms with improved traits faster than traditional methods, and with the development of CRISPR/Cas-based genome editing systems, scientists have a new highly effective tool for creating valuable genotypes. In this review, we summarize the latest research data on poplar diseases, the biology of their pathogens and how these plants resist pathogens. In the final section, we propose to plant male or mixed poplar populations; consider the genes of the MLO group, transcription factors of the WRKY and MYB families and defensive proteins BbChit1, LJAMP2, MsrA2 and PtDef as the most promising targets for genetic engineering; and also pay attention to the possibility of microbiome engineering.

Review: Research progress on seasonal succession of phyllosphere microorganisms

Phyllosphere microorganisms have recently attracted the attention of scientists studying plant microbiomes. The origin, diversity, functions, and interactions of phyllosphere microorganisms have been extensively explored. Many experiments have demonstrated seasonal cycles of phyllosphere microbes. However, a comprehensive comparison of these separate investigations to characterize seasonal trends in phyllosphere microbes of woody and herbaceous plants has not been conducted. In this review, we explored the dynamic changes of phyllosphere microorganisms in woody and non-woody plants with the passage of the season, sought to find the driving factors, summarized these texts, and thought about future research trends regarding the application of phyllosphere microorganisms in agricultural production. Seasonal trends in phyllosphere microorganisms of herbaceous and woody plants have similarities and differences, but extensive experimental validation is needed. Climate, insects, hosts, microbial interactions, and anthropogenic activities are the diverse factors that influence seasonal variation in phyllosphere microorganisms.

Composition, functional, and niche differentiation of fungal communities in the rhizosphere and root endosphere of Cinnamomum migao in southwestern China

AIMS

Roots are key parts of plant material circulation and energy flow, creating two distinct niches for the plant microbiome, such as the rhizosphere and root endosphere, which interact to maintain plant growth and health. In this study, two niches of plant rhizosphere and root endosphere were selected to study the composition and differences of fungi communities in order to better understand how differences in the structure and function of plant fungi communities affect plant health.

METHODS AND RESULTS

The community structure, diversity, and ecological function of fungi in the rhizosphere and root endosphere of Cinnamomum migao were studied using high-throughput sequencing techniques, traditional culture methods, and the FUNGuild database. The results of the analysis of alpha diversity showed that the diversity of rhizosphere fungal communities in C. migao was much higher than that of root endosphere communities. Some similarities and differences were noted between the two niche fungal communities, and some fungi had niche preferences. Functional prediction results demonstrated that fungi in the rhizosphere and root endosphere adopt multiple trophic modes, mostly saprophytic fungi.

CONCLUSIONS

This study provided a basis for an in-depth understanding of the structural variation, niche differentiation, and function of plant root-related fungal microbiota. We believe that it could provide guidance on the subsequent development of beneficial fungi.

Host genomic variation shapes gut microbiome diversity in threespine stickleback fish

IMPORTANCE

A major focus of host-microbe research is to understand how genetic differences, of various magnitudes, among hosts translate to differences in their microbiomes. This has been challenging for animal hosts, including humans, because it is difficult to control environmental variables tightly enough to isolate direct genetic effects on the microbiome. Our work in stickleback fish is a significant contribution because our experimental approach allowed strict control over environmental factors, including standardization of the microbiome from the earliest stage of development and unrestricted co-housing of fish in a truly common environment. Furthermore, we measured host genetic variation over 2,000 regions of the stickleback genome, comparing this information and microbiome composition data among fish from very similar and very different genetic backgrounds. Our findings highlight how differences in the host genome influence microbiome diversity and make a case for future manipulative microbiome experiments that use host systems with naturally occurring genetic variation.

Attribution of dispersal limitation can better explain the assembly patterns of plant microbiota

Disentangling community assembly processes is crucial for fully understanding the function of microbiota in agricultural ecosystems. However, numerous plant microbiome surveys have gradually revealed that stochastic processes dominate the assembly of the endophytic root microbiota in conflict with strong host filtering effects, which is an important issue. Resolving such conflicts or inconsistencies will not only help accurately predict the composition and structure of the root endophytic microbiota and its driving mechanisms, but also provide important guidance on the correlation between the relative importance of deterministic and stochastic processes in the assembly of the root endophytic microbiota, and crop productivity and nutritional quality. Here, we propose that the inappropriate division of dispersal limitation may be the main reason for such inconsistency, which can be resolved after the proportion of dispersal limitation is incorporated into the deterministic processes. The rationality of this adjustment under the framework of the formation of a holobiont between the microbiome and the plant host is herein explained, and a potential theoretical framework for dynamic assembly patterns of endophytic microbiota along the soil-plant continuum is proposed. Considering that the assembly of root endophytic microbiota is complicated, we suggest caution and level-by-level verification from deterministic processes to neutral components to stochastic processes when deciding on the attribution of dispersal limitation in the future to promote the expansion and application of microbiome engineering in sustainable agricultural development based on community assembly patterns.

Affecting Factors of Plant Phyllosphere Microbial Community and Their Responses to Climatic Warming-A Review

Phyllosphere microorganisms are not only an important part of plants, but also an important part of microorganisms. In this review, the function of phyllosphere microorganisms, the assembly mechanism of phyllosphere microorganisms, the driving factors of phyllosphere microbial community structure, and the effects of climate warming on phyllosphere microbial community structure were reviewed. Generally, phyllosphere microorganisms have a variety of functions (e.g., fixing nitrogen, promoting plant growth). Although selection and dispersal processes together regulate the assembly of phyllospheric microbial communities, which one of the ecological processes is dominant and how external disturbances alter the relative contributions of each ecological process remains controversial. Abiotic factors (e.g., climatic conditions, geographical location and physical and chemical properties of soil) and biological factors (e.g., phyllosphere morphological structure, physiological and biochemical characteristics, and plant species and varieties) can affect phyllosphere microbial community structure. However, the predominant factors affecting phyllosphere microbial community structure are controversial. Moreover, how climate warming affects the phyllosphere microbial community structure and its driving mechanism have not been fully resolved, and further relevant studies are needed.

Disentangling arbuscular mycorrhizal fungi and bacteria at the soil-root interface

Arbuscular mycorrhizal fungi (AMF) are essential components of the plant root mycobiome and are found in approximately 80% of land plants. As obligate plant symbionts, AMF harbor their own microbiota, both inside and outside the plant root system. AMF-associated bacteria (AAB) possess various functional traits, including nitrogen fixation, organic and inorganic phosphate mobilization, growth hormone production, biofilm production, enzymatic capabilities, and biocontrol against pathogen attacks, which not only contribute to the health of the arbuscular mycorrhizal symbiosis but also promote plant growth. Because of this, there is increasing interest in the diversity, functioning, and mechanisms that underlie the complex interactions between AMF, AAB, and plant hosts. This review critically examines AMF-associated bacteria, focusing on AAB diversity, the factors driving richness and community composition of these bacteria across various ecosystems, along with the physical, chemical, and biological connections that enable AMF to select and recruit beneficial bacterial symbionts on and within their structures and hyphospheres. Additionally, potential applications of these bacteria in agriculture are discussed, emphasizing the potential importance of AMF fungal highways in engineering plant rhizosphere and endophyte bacteria communities, and the importance of a functional core of AAB taxa as a promising tool to improve plant and soil productivity. Thus, AMF and their highly diverse bacterial taxa represent important tools that could be efficiently explored in sustainable agriculture, carbon sequestration, and reduction of greenhouse gas emissions related to nitrogen fertilizer applications. Nevertheless, future studies adopting integrated multidisciplinary approaches are crucial to better understand AAB functional diversity and the mechanisms that govern these tripartite relationships.

Nitrogen addition alters soil fungal communities, but root fungal communities are resistant to change

Plants are colonized by numerous microorganisms serving important symbiotic functions that are vital to plant growth and success. Understanding and harnessing these interactions will be useful in both managed and natural ecosystems faced with global change, but it is still unclear how variation in environmental conditions and soils influence the trajectory of these interactions. In this study, we examine how nitrogen addition alters plant-fungal interactions within two species of Populus - Populus deltoides and P. trichocarpa. In this experiment, we manipulated plant host, starting soil (native vs. away for each tree species), and nitrogen addition in a fully factorial replicated design. After ~10 weeks of growth, we destructively harvested the plants and characterized plant growth factors and the soil and root endosphere fungal communities using targeted amplicon sequencing of the ITS2 gene region. Overall, we found nitrogen addition altered plant growth factors, e.g., plant height, chlorophyll density, and plant N content. Interestingly, nitrogen addition resulted in a lower fungal alpha diversity in soils but not plant roots. Further, there was an interactive effect of tree species, soil origin, and nitrogen addition on soil fungal community composition. Starting soils collected from Oregon and West Virginia were dominated by the ectomycorrhizal fungi Inocybe (55.8% relative abundance), but interestingly when P. deltoides was grown in its native West Virginia soil, the roots selected for a high abundance of the arbuscular mycorrhizal fungi, Rhizophagus. These results highlight the importance of soil origin and plant species on establishing plant-fungal interactions.

Soil salinity, not plant genotype or geographical distance, shapes soil microbial community of a reed wetland at a fine scale in the Yellow River Delta

Soil salinization is one of the most severe environmental problems restricting biodiversity maintenance and ecosystem functioning in a coastal wetland. Recent studies have well documented how salinization affects soil microbial communities along vegetation succession of coastal wetlands. However, the salinity effect is rarely assessed in the context of plant intraspecific variation. Here, we analyzed the soil bacterial and fungal communities of Phragmites australis wetland using amplicon high-throughput sequencing at a fine scale (within 1000 m) in the Yellow River Delta. Our results revealed that microbial diversity is significantly correlated to soil salinity (assessed as electrical conductivity, EC) but not to soil nutrients (N and P content) or plant intraspecific traits (leaf length, shoot height, and neutral genetic variation). Specifically, the microbial diversity tended to decrease with increased EC, and the bacterial community was more sensitive to EC change than the fungal community. The dominant bacterial phyla were Proteobacteria, Actinobacteria, and Chloroflexi, and the dominant fungal phyla were Ascomycota, Basidiomycota, and Mortierellomycota. The relative abundance of Actinobacteria was significantly negatively correlated to EC, while Proteobacteria were positively correlated to EC. In high salinity (> 1 mS/cm), the role of the stochastic processes became more important in community assembly according to habitat niche breadth estimation, neutral community model, C-score metric, and normalized stochasticity ratio. Additional common garden and microcosm experiments provided evidence that the genotype effect of P. australis on soil microbiome might only occur between lineages from different regions but not from the same region like the Yellow River Delta. Our findings provide new insights into soil microbial community assembly processes with the intraspecific variation of host plants in the wetland ecosystem and offer a scientific reference for salinity mitigation and vegetation management of coastal wetlands under future global changes.

The structure and assembly of rhizobacterial communities are influenced by poplar genotype

The interaction between plants and microbes dominates plant growth and fitness in specific environments. The study of the relationship between plant genotypes and rhizobacterial community structure would provide a deep insight into the recruitment strategies of plants toward soil bacteria. In this study, three genotypes of 18-year-old mature poplar (H1, H2, and H3) derived from four different parents were selected from a germplasm nursery of Populus deltoides. Rhizosphere soil carbon, nitrogen, and phosphorus properties as well as the 16S rDNA sequences of rhizobacterial communities were analyzed to determine the relationship between poplar genotypes and rhizobacterial communities assembly. The results showed there were significant differences in the diversity (Chao1, ACE index, and Shannon index) of rhizobacterial communities between H1 and H2, as well as between H2 and H3, but no difference between H1 and H3. Principal component analysis also revealed a similar structure of rhizobacterial communities between H1 and H3, whereas the rhizobacterial communities of H2 demonstrated significant differences from H1 and H3. Linear discriminant effect size analysis indicated that there were 11 and 14 different biomarkers in the H1 and H3 genotype, respectively, but 42 in the H2 genotype. Co-occurrence network analysis indicated that the rhizobacterial communities of H2 had a distinct network structure compared to those of the other two genotypes, whereas H1 and H3 had a similar pattern of co-occurrence network. Threshold indicator taxa analysis revealed that 63 genera responded significantly to NO3–-N content and 58 genera to NH4+-N/NO3–-N ratio. Moreover, the stochastic assembly process was found to be decreased with increasing NO3–-N content and fluctuated with increasing NH4+-N/NO3–-N ratio. All results indicated that the structure of poplar rhizobacterial communities were influenced by host genotypes, and available nitrogen might play a dominant role in the assembly of rhizobacterial communities. This study would promote the future selection and utilization of rhizobacteria in poplar breeding.

Relationships between Sphaerulina musiva Infection and the Populus Microbiome and Metabolome

Pathogenic fungal infections in plants may, in some cases, lead to downstream systematic impacts on the plant metabolome and microbiome that may either alleviate or exacerbate the effects of the fungal pathogen. While Sphaerulina musiva is a well-characterized fungal pathogen which infects Populus tree species, an important wood fiber and biofuel feedstock, little is known about its systematic effects on the metabolome and microbiome of Populus. Here, we investigated the metabolome of Populus trichocarpa and Populus deltoides leaves and roots and the microbiome of the leaf and root endospheres, phylloplane, and rhizosphere to understand the systematic impacts of S. musiva abundance and infection on Populus species in a common garden field setting. We found that S. musiva is indeed present in both P. deltoides and P. trichocarpa, but S. musiva abundance was not statistically related to stem canker onset. We also found that the leaf and root metabolomes significantly differ between the two Populus species and that certain leaf metabolites, particularly the phenolic glycosides salirepin and salireposide, are diminished in canker-infected P. trichocarpa trees compared to their uninfected counterparts. Furthermore, we found significant associations between the metabolome, S. musiva abundance, and microbiome composition and α-diversity, particularly in P. trichocarpa leaves. Our results show that S. musiva colonizes both resistant and susceptible hosts and that the effects of S. musiva on susceptible trees are not confined to the site of canker infection. IMPORTANCE Poplar (Populus spp.) trees are ecologically and economically important trees throughout North America. However, many western North American poplar plantations are at risk due to the introduction of the nonnative fungal pathogen Sphaerulina musiva, which causes leaf spot and cankers, limiting their production. To better understand the interactions among the pathogen S. musiva, the poplar metabolome, and the poplar microbiome, we collected leaf, root, and rhizosphere samples from poplar trees consisting of 10 genotypes and two species with differential resistance to S. musiva in a common garden experiment. Here, we outline the nuanced relationships between the poplar metabolome, microbiome, and S. musiva, showing that S. musiva may affect poplar trees in tissues distal to the site of infection (i.e., stem). Our research contributes to improving the fundamental understanding of S. musiva and Populus sp. ecology and the utility of a holobiont approach in understanding plant disease.

Spatio-temporal variation in the root-associated microbiota of orchard-grown apple trees

BACKGROUND

The root-associated microbiome has been of keen research interest especially in the last decade due to the large potential for increasing overall plant performance in agricultural systems. Studies about spatio-temporal variation of the root-associated microbiome focused so far primarily on community-compositional changes of annual plants, while little is known about their perennial counterparts. The aim of this work was to get deep insight into the spatial patterns and temporal dynamics of the root associated microbiota of apple trees.

RESULTS

The bacterial community structure in rhizospheric soil and endospheric root material from orchard-grown apple trees was characterized based on 16S rRNA gene amplicon sequencing. At the small scale, the rhizosphere and endosphere bacterial communities shifted gradually with increasing root size diameter (PERMANOVA R²-values up to 0.359). At the larger scale, bulk soil heterogeneity introduced variation between tree individuals, especially in the rhizosphere microbiota, while the presence of a root pathogen was contributing to tree-to-tree variation in the endosphere microbiota. Moreover, the communities of both compartments underwent seasonal changes and displayed year-to-year variation (PERMANOVA R²-values of 0.454 and 0.371, respectively).

CONCLUSIONS

The apple tree root-associated microbiota can be spatially heterogeneous at field scale due to soil heterogeneities, which particularly influence the microbiota in the rhizosphere soil, resulting in tree-to-tree variation. The presence of pathogens can contribute to this variation, though primarily in the endosphere microbiota. Smaller-scale spatial heterogeneity is observed in the rhizosphere and endosphere microbiota related to root diameter, likely influenced by root traits and processes such as rhizodeposition. The microbiota is also subject to temporal variation, including seasonal effects and annual variation. As a consequence, responses of the tree root microbiota to further environmental cues should be considered in the context of this spatio-temporal variation.

Maize root-associated niches determine the response variation in bacterial community assembly and function to phthalate pollution

Plant root-associated microbiome can be influenced by environmental stress like pollution. However, how organic pollution influences microbial communities in different root-associated niches and plant-microbe interaction remains unclear. We analyzed maize root-associated bacterial communities under stress of di-(2-ethylhexyl) phthalate (DEHP). The results demonstrate that structures and functions of bacterial communities are significantly different among four root-associated niches, and bacterial diversities gradually decline along bulk soil - rhizosphere - rhizoplane - endosphere. DEHP stress significantly reduces bacterial community diversities in both rhizosphere and rhizoplane, and changes their composition, enrichment and depleting process. DEHP stress led to the enrichment of some specific bacterial taxa like phthalate-degrading bacteria (e.g., Rhizobium and Agromyces) and functional genes involving in phthalate degradation (e.g., pht3 and pcaG). Notably, rhizoplane bacterial community is more sensitive to DEHP stress by enriching stress-resistant bacteria and more complex microbial network on rhizoplane than in rhizosphere. DEHP stress also disturbs the colonization and biofilm forming of root-associated bacteria on rhizoplane. Rhizoplane bacterial community is significantly correlated with maize growth while negatively influenced by DEHP stress. DEHP stress negatively influences plant-microbe interaction and inhibits maize growth. This study provides deep and comprehensive understanding for root-associated bacterial community in response to organic pollution.