Microbial functional traits in phyllosphere are more sensitive to anthropogenic disturbance than in soil

Response of microbial communities and biogeochemical cycling functions to sediment physicochemical properties and microplastic pollution under damming and water diversion projects

Understanding the interactions among flow-sediment, microorganisms, and biogeochemical cycles is crucial for comprehending the ecological response mechanisms of dams and water diversion. This study focused on the spatial patterns of carbon, nitrogen, phosphorus, and sulfur (CNPS) cycle functional genes in the water resource for the middle route of the South-to-North Water Diversion Project in China, specifically the Danjiangkou Reservoir (comprising the Han and Dan reservoirs). The investigation incorporated sediment physicochemical properties and microplastic pollution. Numerous microbial species were identified, revealing that microbial communities demonstrated sensitivity to changes in sedimentary mud content. The communities exhibited greater β diversity due to finer sediment particles in the Han Reservoir (HR), whereas in the Dan Reservoir (DR), despite having higher sediment nutrient content and MPs pollution, did not display this pattern. Regarding the composition and structure of microbial communities, the study highlighted that sediment N and P content had a more significant influence compared to particle size and MPs. The quantitative microbial element cycling (QMEC) results confirmed the presence of extensive chemolithotrophic microbes and strong nitrogen cycle activity stemming from long-term water storage and diversion operations. The denitrification intensity in the HR surpassed that of the DR. Notably, near the pre-dam area, biological nitrogen fixation, phosphorus removal, and sulfur reduction exhibited noticeable increases. Dam construction refined sediment, fostering the growth of different biogeochemical cycling bacteria and increasing the abundance of CNPS cycling genes. Furthermore, the presence of MPs exhibited a positive correlation with S cycling genes and a negative correlation with C and N cycling genes. These findings suggest that variations in flow-sediment dynamics and MPs pollution have significant impact the biogeochemical cycle of the reservoir.

Deciphering the environmental adaptation and functional trait of core and noncore bacterial communities in impacted coral reef seawater

Microorganisms play pivotal roles in different biogeochemical cycles within coral reef waters. Nevertheless, our comprehension of the microbially mediated processes following environmental perturbation is still limited. To gain a deeper insight into the environmental adaptation and nutrient cycling, particularly within core and noncore bacterial communities, it is crucial to understand reef ecosystem functioning. In this study, we delved into the microbial community structure and function of seawater in a coral reef under different degrees of anthropogenic disturbance. To achieve this, we harnessed the power of 16S rRNA gene high-throughput sequencing and metagenomics techniques. The results showed that a continuous temporal succession but little spatial heterogeneity in the bacterial communities of core and noncore taxa and functional profiles involved in nitrogen (N) and phosphorus (P) cycling. Eutrophication state (i.e., nutrient concentration and turbidity) and temperature played pivotal roles in shaping both the microbial community composition and functional traits of coral reef seawater. Within this context, the core subcommunity exhibited a remarkably broader habitat niche breadth, stronger phylogenetic signal and lower environmental sensitivity when compared to the noncore taxa. Null model analysis further revealed that the core subcommunity was governed primarily by stochastic processes, while deterministic processes played a more significant role in shaping the noncore subcommunity. Furthermore, our observations indicated that changes in function related to N cycling were correlated to the variations in noncore taxa, while core taxa played a more substantial role in critical processes such as P cycling. Collectively, these findings facilitated our knowledge about environmental adaptability of core and noncore bacterial taxa and shed light on their respective roles in maintaining diverse nutrient cycling within coral reef ecosystems.

Nitrogen fertilization modulates rice phyllosphere functional genes and pathogens through fungal communities

The phyllosphere is a vital yet often neglected habitat hosting diverse microorganisms with various functions. However, studies regarding how the composition and functions of the phyllosphere microbiome respond to agricultural practices, like nitrogen fertilization, are limited. This study investigated the effects of long-term nitrogen fertilization with different levels (CK, N90, N210, N330) on the functional genes and pathogens of the rice phyllosphere microbiome. Results showed that the relative abundance of many microbial functional genes in the rice phyllosphere was significantly affected by nitrogen fertilization, especially those involved in C fixation and denitrification genes. Different nitrogen fertilization levels have greater effects on fungal communities than bacteria communities in the rice phyllosphere, and network analysis and structural equation models further elucidate that fungal communities not only changed bacterial-fungal inter-kingdom interactions in the phyllosphere but also contributed to the variation of biogeochemical cycle potential. Besides, the moderate nitrogen fertilization level (N210) was associated with an enrichment of beneficial microbes in the phyllosphere, while also resulting in the lowest abundance of pathogenic fungi (1.14 %). In contrast, the highest abundance of pathogenic fungi (1.64 %) was observed in the highest nitrogen fertilization level (N330). This enrichment of pathogen due to high nitrogen level was also regulated by the fungal communities, as revealed through SEM analysis. Together, we demonstrated that the phyllosphere fungal communities were more sensitive to the nitrogen fertilization levels and played a crucial role in influencing phyllosphere functional profiles including element cycling potential and pathogen abundance. This study expands our knowledge regarding the role of phyllosphere fungal communities in modulating the element cycling and plant health in sustainable agriculture.

Assembly and succession of the phyllosphere microbiome and nutrient-cycling genes during plant community development in a glacier foreland

The phyllosphere, particularly the leaf surface of plants, harbors a diverse range of microbiomes that play a vital role in the functioning of terrestrial ecosystems. However, our understanding of microbial successions and their impact on functional genes during plant community development is limited. In this study, considering core and satellite microbial taxa, we characterized the phyllosphere microbiome and functional genes in various microhabitats (i.e., leaf litter, moss and plant leaves) across the succession of a plant community in a low-altitude glacier foreland. Our findings indicate that phyllosphere microbiomes and associated ecosystem stability increase during the succession of the plant community. The abundance of core taxa increased with plant community succession and was primarily governed by deterministic processes. In contrast, satellite taxa abundance decreased during plant community succession and was mainly governed by stochastic processes. The abundance of microbial functional genes (such as C, N, and P hydrolysis and fixation) in plant leaves generally increased during the plant community succession. However, in leaf litter and moss leaves, only a subset of functional genes (e.g., C fixation and degradation, and P mineralization) showed a tendency to increase with plant community succession. Ultimately, the community of both core and satellite taxa collaboratively influenced the characteristics of phyllosphere nutrient-cycling genes, leading to the diverse profiles and fluctuating abundance of various functional genes during plant community succession. These findings offer valuable insights into the phyllosphere microbiome and plant-microbe interactions during plant community development, advancing our understanding of the succession and functional significance of the phyllosphere microbial community.

Organic amendments modulate the crop yield and rhizospheric bacterial community diversity: a 3-year field study with Cajanus cajan

Excessive use of chemicals to enhance soil nutrient status and crop yield has resulted in a decline in soil health. Organic farming promotes organic amendments, which help to balance the ecosystem. Understanding the dynamic patterns of belowground microbial populations is essential for developing sustainable agricultural systems. Therefore, the study was designed to evaluate the effect of different agri-practices on rhizospheric bacterial diversity and crop yield in an Indian agricultural system. A 3-year field experiment was set up in a randomized block design using Cajanus cajan as a model crop, comparing conventional farming with organic practice (with animal manure and bio-compost as amendments). Plant and rhizospheric soil samples were collected at the harvest stage for assessing various growth attributes, and for characterizing rhizospheric bacterial diversity. Enhanced crop productivity was seen in conventional farming, with a 2.2-fold increase in grain yield over control. However, over the 3 years, an overall positive impact was observed in the bio-compost-based organic amendment, in terms of bacterial abundance, over other treatments. At the harvest stage of the third cropping season, the bacterial diversity in the organic treatments showed little similarity to the initial bacterial community composition of the amendment applied, indicating stabilization along the growth cycles. The study emphasizes the significance of the choice of the amendment for ushering in agricultural sustainability.

Analysis of diversity and function of epiphytic bacterial communities associated with macrophytes using a metagenomic approach

Epiphytic bacteria constitute a vital component of aquatic ecosystems, pivotal in regulating elemental cycling. Despite their significance, the diversity and functions of epiphytic bacterial communities adhering to various submerged macrophytes remain largely unexplored. In this study, we employed a metagenomic approach to investigate the diversity and function of epiphytic bacterial communities associated with six submerged macrophytes: Ceratophyllum demersum, Hydrilla verticillata, Myriophyllum verticillatum, Potamogeton lucens, Stuckenia pectinata, and Najas marina. The results revealed that the predominant epiphytic bacterial species for each plant type included Pseudomonas spp., Microbacterium spp., and Stenotrophomonas rhizophila. Multiple comparisons and linear discriminant analysis effect size indicated a significant divergence in the community composition of epiphytic bacteria among the six submerged macrophytes, with 0.3-1% of species uniquely identified. Epiphytic bacterial richness associated with S. pectinata significantly differed from that of both C. demersum and H. verticillata, although no significant differences were observed in diversity and evenness. Functionally, notable variations were observed in the relative abundances of genes associated with carbon, nitrogen, and phosphorus cycling within epiphytic bacterial communities on the submerged macrophyte hosts. Among these communities, H. verticillata exhibited enrichment in genes related to the 3-hydroxypropionate bicycle and nitrogen assimilation, translocation, and denitrification. Conversely, M. verticillatum showcased enrichment in genes linked to the reductive citric acid cycle (Arnon-Buchanan cycle), reductive pentose phosphate cycle (Calvin cycle), polyphosphate degradation, and organic nitrogen metabolism. In summary, our findings offer valuable insights into the diversity and function of epiphytic bacteria on submerged macrophyte leaves, shedding light on their roles in lake ecosystems.

Core community drives phyllosphere bacterial diversity and function in multiple ecosystems

The phyllosphere provides a habitat for a large sum of microorganisms which are modulated by numerous biotic and abiotic factors. While it is logical that host lineage must have some effect on the phyllosphere habitat, it is unclear if phyllospheres harbor similar microbial core communities across multiple ecosystems at the continental-scale. Here we collected 287 phyllosphere bacterial communities from seven ecosystems (including paddy field, dryland, urban area, protected agricultural land, forest, wetland, and grassland) in east-China to identify the regional core community and to characterize the importance of such communities in maintaining phyllosphere bacterial community structure and function. Despite significantly different bacterial richness and structure, the seven studied ecosystems contained a similar regional core community of 29 OTUs that comprised 44.9 % of the total bacterial abundance. The regional core community was less affected by environmental variables and less connected in the co-occurrence network compared with other non-core OTUs (the whole minus regional core community). Furthermore, the regional core community also had a large proportion (>50 %) of a constrained set of nutrient metabolism related functional potentials and less functional redundancy. This study suggests there is a robust regional core phyllosphere community regardless of ecosystem or spatial and environmental heterogeneity, and supports the argument that core communities are pivotal in maintaining microbial community structure and function.

Phyllosphere Microbiome in Plant Health and Disease

The phyllosphere refers to the aboveground surface of plants colonized by diverse microorganisms. Microbes inhabiting this environment play an important role in enhancing the host's genomic and metabolic capabilities, including defense against pathogens. Compared to the large volume of studies on rhizosphere microbiome for plant health and defense, our understanding of phyllosphere microbiome remains in its infancy. In this review, we aim to explore the mechanisms that govern the phyllosphere assembly and their function in host defence, as well as highlight the knowledge gaps. These efforts will help develop strategies to harness the phyllosphere microbiome toward sustainable crop production.

Urban greenspace types influence the microbial community assembly and antibiotic resistome more in the phyllosphere than in the soil

Urban greenspace (UGS) is recognized to confer significant societal benefits, but few studies explored the microbial communities and antibiotic resistance genes (ARGs) from different urban greenspace types. Here, we collected leaf and soil samples from forest, greenbelt, and parkland to analyze microbial community assembly and ARG profile. For phyllosphere fungal community, the α-diversity was higher in forest, compared to those in greenbelt and parkland. Moreover, urban greenspace types altered the community assembly. Stochastic processes had a greater effect on phyllosphere fungal community in greenbelt and parkland, while in forest they were dominated by deterministic processes. In contrast, no significant differences in bacterial community diversity, community assembly were observed between the samples collected from different urban greenspace types. A total of 153 ARGs and mobile genetic elements (MGEs) were detected in phyllosphere and soil with resistance to the majority classes of antibiotics commonly applied to humans and animals. Structural equation model further revealed that a direct association between greenspace type and ARGs in the phyllosphere even after considering the effects of all other factors simultaneously. Our findings provide new insights into the microbial communities and antibiotic resistome of urban greenspaces and the potential risk linked with human health.

Response of coral bacterial composition and function to water quality variations under anthropogenic influence

Microbial communities play key roles in the adaptation of corals living in adverse environments, as the microbiome flexibility can enhance environmental plasticity of coral holobiont. However, the ecological association of coral microbiome and related function to locally deteriorating water quality remains underexplored. In this work, we used 16S rRNA gene sequencing and quantitative microbial element cycling (QMEC) to investigate the seasonal changes of bacterial communities, particularly their functional genes related to carbon (C), nitrogen (N), phosphorus (P) and sulfur (S) cycle, of the scleractinian coral Galaxea fascicularis from nearshore reefs exposed anthropogenic influence. We used nutrient concentrations as the indicator of anthropogenic activities in coastal reefs, and found a higher nutrient pressure in spring than summer. The bacterial diversity, community structure and dominant bacteria of coral shifted significantly due to seasonal variations dominated by nutrient concentrations. Additionally, the network structure and nutrient cycling gene profiles in summer under low nutrient stress was distinct from that under poor environmental conditions in spring, with lower network complexity and abundance of CNPS cycling genes in summer compared with spring. We further identified significant correlations between microbial community (taxonomic composition and co-occurrence network) and geochemical functions (abundance of multiple functional genes and functional community). Nutrient enrichment was proved to be the most important environmental fluctuation in controlling the diversity, community structure, interactional network and functional genes of the coral microbiome. These results highlight that seasonal shifts in coral-associated bacteria due to anthropogenic activities alter the functional potentials, and provide novel insight about the mechanisms of coral adaptation to locally deteriorating environments.

Contrasting response strategies of microbial functional traits to polycyclic aromatic hydrocarbons contamination under aerobic and anaerobic conditions

PAHs (Polycyclic aromatic hydrocarbons) are widely distributed in soil ecosystems, but our knowledge regarding the impacts of PAHs effects on soil microbial functional traits is limited. In this study, we evaluated the response and regulating strategies of microbial functional traits that are associated with the typical C, N, P, S cycling processes in a pristine soil under aerobic and anaerobic conditions after the addition of PAHs. Results revealed that indigenous microorganisms had strong degradation potential and adaptability to PAHs especially under aerobic conditions, while anaerobic conditions favored the degradation of high molecular weight PAHs. PAHs exhibited contrasting effects on soil microbial functional traits under different aeration conditions. It would probably change microbial carbon source utilization preference, stimulate inorganic P solubilization and strengthen the functional interactions between soil microorganisms under aerobic conditions, while might cause the increase of H₂S and CH₄ emissions under anaerobic conditions. This research provides an effective theoretical support for the ecological risk assessment of soil PAHs pollution.

Potential effects of micro- and nanoplastics on phyllosphere microorganisms and their evolutionary and ecological responses

Plastic pollution is among the most urgent environmental and social challenges of the 21st century, and their influxes in the environment have altered critical growth drivers in all biomes, attracting global concerns. In particular, the consequences of microplastics on plants and their associated soil microorganisms have gained a large audience. On the contrary, how microplastics and nanoplastics (M/NPs) may influence the plant-associated microorganisms in the phyllosphere (i.e., the aboveground portion of plants) is nearly unknown. We, therefore, summarize evidence that may potentially connect M/NPs, plants, and phyllosphere microorganisms based on studies on other analogous contaminants such as heavy metals, pesticides, and nanoparticles. We show seven pathways that may link M/NPs into the phyllosphere environment, and provide a conceptual framework explaining the direct and indirect (soil legacy) effects of M/NPs on phyllosphere microbial communities. We also discuss the adaptive evolutionary and ecological responses, such as acquiring novel resistance genes via horizontal gene transfer and microbial degradation of plastics of the phyllosphere microbial communities, to M/NPs-induced threats. Finally, we highlight the global consequences (e.g., disruption of ecosystem biogeochemical cycling and impaired host-pathogen defense chemistry that can lead to reduced agricultural productivity) of altered plant-microbiome interactions in the phyllosphere in the context of a predicted surge of plastic production and conclude with pending questions for future research priorities. In conclusion, M/NPs are very likely to produce significant effects on phyllosphere microorganisms and mediate their evolutionary and ecological responses.

Changes in the structure and function of rhizosphere soil microbial communities induced by Amaranthus palmeri invasion

Introduction

Plant invasion can profoundly alter ecosystem processes driven by microorganisms. The fundamental mechanisms linking microbial communities, functional genes, and edaphic characteristics in invaded ecosystems are, nevertheless, poorly understood.

Methods

Here, soil microbial communities and functions were determined across 22 Amaranthus palmeri (A. palmeri) invaded patches by pairwise 22 native patches located in the Jing-Jin-Ji region of China using high-throughput amplicon sequencing and quantitative microbial element cycling technologies.

Results

As a result, the composition and structure of rhizosphere soil bacterial communities differed significantly between invasive and native plants according to principal coordinate analysis. A. palmeri soils exhibited higher abundance of Bacteroidetes and Nitrospirae, and lower abundance of Actinobacteria than native soils. Additionally, compared to native rhizosphere soils, A. palmeri harbored a much more complex functional gene network with higher edge numbers, average degree, and average clustering coefficient, as well as lower network distance and diameter. Furthermore, the five keystone taxa identified in A. palmeri rhizosphere soils belonged to the orders of Longimicrobiales, Kineosporiales, Armatimonadales, Rhizobiales and Myxococcales, whereas Sphingomonadales and Gemmatimonadales predominated in the native rhizosphere soils. Moreover, random forest model revealed that keystone taxa were more important indicators of soil functional attributes than edaphic variables in both A. palmeri and native rhizosphere soils. For edaphic variables, only ammonium nitrogen was a significant predictor of soil functional potentials in A. palmeri invaded ecosystems. We also found keystone taxa in A. palmeri rhizosphere soils had strong and positive correlations with functional genes compared to native soils.

Discussion

Our study highlighted the importance of keystone taxa as a driver of soil functioning in invaded ecosystem.

Plant identity shapes phyllosphere microbiome structure and abundance of genes involved in nutrient cycling

The phyllosphere is a fluctuant micro-environment habitat that harbors diverse microbial communities that have the potential to influence plant growth through their effect on host fitness. However, we know little about the driving factors of phyllosphere microbial functional traits, e.g., genes related to nutrient cycling and microbial community structure under anthropic disturbance. Here, we characterized phyllosphere microbial communities and the abundance of genes related to nutrient cycling from diverse plant species between urban and natural habitats. We measured leaf functional traits to investigate the potential drivers of the phyllosphere microbial profile. Results indicated that phyllosphere microbial communities differed significantly between urban and natural habitats, and that this variation was dependent upon plant species. Host plant species had a greater influence on the abundance of genes involved in nutrient cycling in the phyllosphere than habitat. In addition, phyllosphere microbial diversity and functional gene abundance were significantly correlated. Furthermore, host leaf functional traits (e.g., specific leaf area and nutrient content) were potential driving factors of both phyllosphere microbial community structure and the abundance of genes involved in nutrient cycling. These findings contribute to a better understanding of the phyllosphere microbiome and its biotic and abiotic controlling factors, which improves our understanding of plant-microbe interactions and their ecosystem functions under anthropic disturbance.

Urbanization Reduces Phyllosphere Microbial Network Complexity and Species Richness of Camphor Trees

Studies on microbial communities associated with foliage in natural ecosystems have grown in number in recent years yet have rarely focused on urban ecosystems. With urbanization, phyllosphere microorganisms in the urban environment have come under pressures from increasing human activities. To explore the effects of urbanization on the phyllosphere microbial communities of urban ecosystems, we investigated the phyllosphere microbial structure and the diversity of camphor trees in eight parks along a suburban-to-urban gradient. The results showed that the number of ASVs (amplicon sequence variants), unique on the phyllosphere microbial communities of three different urbanization gradients, was 4.54 to 17.99 times higher than that of the shared ASVs. Specific microbial biomarkers were also found for leaf samples from each urbanization gradient. Moreover, significant differences (R² = 0.133, p = 0.005) were observed in the phyllosphere microbial structure among the three urbanization gradients. Alpha diversity and co-occurrence patterns of bacterial communities showed that urbanization can strongly reduce the complexity and species richness of the phyllosphere microbial network of camphor trees. Correlation analysis with environmental factors showed that leaf total carbon (C), nitrogen (N), and sulfur (S), as well as leaf C/N, soil pH, and artificial light intensity at night (ALIAN) were the important drivers in determining the divergence of phyllosphere microbial communities across the urbanization gradient. Together, we found that urbanization can affect the composition of the phyllosphere bacterial community of camphor trees, and that the interplay between human activities and plant microbial communities may contribute to shaping the urban microbiome.

Successions and interactions of phyllospheric microbiome in response to NH3 exposure

Phyllosphere and numerous phyllospheric microbiomes present a huge potential for air pollution mitigation. Despite research investigating the microbial compositions in the phyllosphere, the successions and interactions of the phyllospheric microbiome under ammonia gas (NH₃) stress remain poorly understood. Herein, we performed 16S rDNA, the internal transcribed spacer (ITS) profiling and a quantitative microbial element cycling (QMEC) method to reveal successions, co-occurrence, and N-cycling functions changes of phyllospheric bacteria and fungi during NH₃ exposure. The NH₃ input mainly elevated ammonium (NH₄⁺-N) and total nitrogen (TN) levels on the leaf surface. The exposure in the phyllosphere decreased fungal concentration with a homogeneity increase while enhanced bacterial concentration with a noticeable richness drop. Both short-term (2-week) and long-term (6-week) exposure induced significant changes in microbial compositions. Bacterial genera (Nocardioides, Pseudonocardia) and fungal genera (Alternaria, Acremonium) dominated throughout the exposure. Intensive microbial interactions compared to that in the natural phyllosphere were observed via network analysis. Our results showed that N-cycling functional genes were largely stimulated by the exposure and might, in turn contribute to NH₃ pollution buffer and alleviation via microbial metabolism. This study extended the knowledge on microbial responses to NH₃ exposure in the phyllosphere and enlightened phylloremediation on NH₃ through the microbial role.

Bio-fertilizer Amendment Alleviates the Replanting Disease under Consecutive Monoculture Regimes by Reshaping Leaf and Root Microbiome

Replanting disease is a growing problem in intensive agricultural systems. Application of bio-fertilizer containing beneficial microbes contributes to disease suppression and is a promising strategy to control replanting disease. However, the effect of both replanting disease and bio-fertilizer amendment on the assembly of crop microbiota in leaves and roots and their relationships to crop yield and quality remains elusive. In these experiments, roots and leaves of Radix pseudostellariae were collected from different consecutive monoculture and bio-fertilizer amended fields, and the associated microbiota were characterized by bacterial 16S rRNA gene sequencing and quantitative PCR. Consecutive monoculture altered the bacterial community structure and composition and significantly increased the abundance of potential pathogenic Ralstonia and Fusarium oxysporum in leaves and roots. Furthermore, bio-fertilizer application alleviated replanting disease by decreasing the pathogen load, increasing the potential beneficial genera Pseudomonas, Streptomyces, Paenibacillus, and Bradyrhizobium. The proportion of positive correlations in the co-occurrence network of bio-fertilizer application was the highest, implying that bio-fertilizer potentially enhanced ecological commensalism or mutualism of the bacterial community across the two compartments. Structural equation models indicated that bio-fertilizer had a positive and indirect effect on both yield and quality by shaping the leaf microbiota and the root microbiota. Our findings highlight the role of leaf and root microbiota on replanting disease, showing that bio-fertilizer contributes to alleviating replanting disease by improving microbe-microbe interactions.

Variations of Phyllosphere and Rhizosphere Microbial Communities of Pinus koraiensis Infected by Bursaphelenchus xylophilus

Pine wood nematode, Bursaphelenchus xylophilus, as one of the greatest threats to pine trees, is spreading all over the world. Plant microorganisms play an important role in the pathogenesis of nematodes. The phyllosphere and rhizosphere bacterial and fungal communities associated with healthy Pinus koraiensis (PKa) and P. koraiensis infected by B. xylophilus at the early (PKb) and last (PKc) stages were analyzed. Our results demonstrated that pine wood nematode (PWD) could increase the phyllosphere bacterial Pielou_e, Shannon, and Simpson index; phyllosphere fungal Chao 1 index, as well as rhizosphere bacterial Pielou_e, Shannon, and Simpson index; and rhizosphere fungal Pielou_e, Shannon, and Simpson index. What's more, slight shifts of the microbial diversity were observed at the early stage of infection, and the microbial diversity increased significantly as the symptoms of infection worsened. With the infection of B. xylophilus in P. koraiensis, Bradyrhizobium (rhizosphere bacteria), Massilia (phyllosphere bacteria), and Phaeosphaeriaceae (phyllosphere fungi) were the major contributors to the differences in community compositions among different treatments. With the infection of PWD, most of the bacterial groups tended to be co-excluding rather than co-occurring. These changes would correlate with microbial ability to suppress plant pathogen, enhancing the understanding of disease development and providing guidelines to pave the way for its possible management.

Water stress and disruption of mycorrhizas induce parallel shifts in phyllosphere microbiome composition

Water and nutrient acquisition are key drivers of plant health and ecosystem function. These factors impact plant physiology directly as well as indirectly through soil- and root-associated microbial responses, but how they in turn affect aboveground plant-microbe interactions are not known. Through experimental manipulations in the field and growth chamber, we examine the interacting effects of water stress, soil fertility, and arbuscular mycorrhizal fungi on bacterial and fungal communities of the tomato (Solanum lycopersicum) phyllosphere. Both water stress and mycorrhizal disruption reduced leaf bacterial richness, homogenized bacterial community composition among plants, and reduced the relative abundance of dominant fungal taxa. We observed striking parallelism in the individual microbial taxa in the phyllosphere affected by irrigation and mycorrhizal associations. Our results show that soil conditions and belowground interactions can shape aboveground microbial communities, with important potential implications for plant health and sustainable agriculture.

Deyeuxia angustifolia Kom. encroachment changes soil physicochemical properties and microbial community in the alpine tundra under climate change

Plant encroachment in alpine regions, caused by global changes and human activities, has been well documented. However, our knowledge of the effects of plant encroachment on belowground microbial communities is limited. Here, we investigated soil physicochemical properties and microbial community structures under the impact of plant encroachment along an elevation gradient in the alpine tundra of the Changbai Mountain, China. We found that plant encroachment had insignificant (P > 0.05) and inconsistent effects on the α-diversity (number of observed OTUs, Shannon, Chao1, Faith's PD) of soil microbial communities. Plant encroachment indirectly influenced soil microbial community structures by altering soil physicochemical properties, which differed between elevations and plant types (P < 0.05). In all, 40 bacterial indicator taxa and 57 fungal indicator taxa significantly shifted in response to plant encroachment, some of which were involved in soil biogeochemical cycle. Overall, our results documented the impacts of plant encroachment on soil microbial diversity and community composition, and provided a scientific basis for predicting future changes in alpine ecosystem structure and function and its subsequent feedbacks to global change.

Precipitation increases the abundance of fungal plant pathogens in Eucalyptus phyllosphere

Understanding the current and future distributions of plant pathogens is critical to predict the plant performance and related economic benefits in the changing environment. Yet, little is known about the roles of environmental drivers in shaping the profiles of fungal plant pathogens in phyllosphere, an important habitat of microbiomes on Earth. Here, using a large-scale investigation of Eucalyptus phyllospheric microbiomes in Australia and the multiple linear regression model, we show that precipitation is the most important predictor of fungal taxonomic diversity and abundance. The abundance of fungal plant pathogens in phyllosphere exhibited a positive linear relationship with precipitation. With this empirical dataset, we constructed current and future atlases of phyllosphere plant pathogens to estimate their spatial distributions under different climate change scenarios. Our atlases indicate that the abundance of fungal plant pathogens would increase especially in the coastal regions with up to 100-fold increase compared with the current abundance. These findings advance our understanding of the distributions of fungal plant pathogens in phyllospheric microbiomes under the climate change, which can improve our ability to predict and mitigate their impacts on plant productivity and economic losses.

Comparative Metagenomics Reveals Microbial Signatures of Sugarcane Phyllosphere in Organic Management

Converting conventional farms to organic systems to improve ecosystem health is an emerging trend in recent decades, yet little is explored to what extent and how this process drives the taxonomic diversity and functional capacity of above-ground microbes. This study was, therefore, conducted to investigate the effects of agricultural management, i.e., organic, transition, and conventional, on the structure and function of sugarcane phyllosphere microbial community using the shotgun metagenomics approach. Comparative metagenome analysis exhibited that farming practices strongly influenced taxonomic and functional diversities, as well as co-occurrence interactions of phyllosphere microbes. A complex microbial network with the highest connectivity was observed in organic farming, indicating strong resilient capabilities of its microbial community to cope with the dynamic environmental stressors. Organic farming also harbored genus Streptomyces as the potential keystone species and plant growth-promoting bacteria as microbial signatures, including Mesorhizobium loti, Bradyrhizobium sp. SG09, Lactobacillus plantarum, and Bacillus cellulosilyticus. Interestingly, numerous toxic compound-degrading species were specifically enriched in transition farming, which might suggest their essential roles in the transformation of conventional to organic farming. Moreover, conventional practice diminished the abundance of genes related to cell motility and energy metabolism of phyllosphere microbes, which could negatively contribute to lower microbial diversity in this habitat. Altogether, our results demonstrated the response of sugarcane-associated phyllosphere microbiota to specific agricultural managements that played vital roles in sustainable sugarcane production.