Host identity is more important in structuring bacterial epiphytes than endophytes in a tropical mangrove forest

Differentiation and Interconnection of the Bacterial Community Associated with Silene nigrescens Along the Soil-To-Plant Continuum in the Sub-Nival Belt of the Qiangyong Glacier

Plant microbiomes provide significant fitness advantages to their plant hosts, especially in the sub-nival belt. Studies to date have primarily focused on belowground communities in this region. Here, we utilized high-throughput DNA sequencing to quantify bacterial communities in the rhizosphere soil as well as in the root and leaf endosphere compartments of Silene nigrescens to uncover the differentiation and interconnections of these bacterial communities along the soil-to-plant continuum. Our findings reveal that the bacterial communities exhibit notable variation across different plant compartment niches: the rhizosphere soil, root endosphere, and leaf endosphere. There was a progressive decline in diversity, network complexity, network modularity, and niche breadth from the rhizosphere soil to the root endosphere, and further to the leaf endosphere. Conversely, both the host plant selection effect and the stability of these communities showed an increasing trend. Total nitrogen and total potassium emerged as crucial factors accounting for the observed differences in diversity and composition, respectively. Additionally, 3.6% of the total amplicon sequence variants (ASVs) were shared across the rhizosphere soil, root endosphere, and leaf endosphere. Source-tracking analysis further revealed bacterial community migration among these compartments. The genera Pseudomonas, IMCC26256, Mycobacterium, Phyllobacterium, and Sphingomonas constituted the core of the bacterial microbiome. These taxa are shared across all three compartment niches and function as key connector species. Notably, Pseudomonas stands out as the predominant taxon among these bacteria, with nitrogen being the most significant factor influencing its relative abundance. These findings deepen our understanding of the assembly principles and ecological dynamics of the plant microbiome in the sub-nival belt, offering an integrated framework for its study.

Host selection is not a universal driver of phyllosphere community assembly among ecologically similar native New Zealand plant species

BACKGROUND

A growing body of evidence demonstrates that host-associated microbial communities of plant leaf surfaces (i.e. the phyllosphere) can influence host functional traits. However, it remains unclear whether host selection is a universal driver of phyllosphere community assembly. We targeted mānuka (Leptospermum scoparium) and three neighbouring non-mānuka plant species along an 1800-m transect in a New Zealand native bush to conduct a hypothesis-driven investigation of the relative influence of host species identity and stochastic dispersal on the composition of natural phyllosphere bacterial communities.

RESULTS

We detected significant correlations between host species identity and mānuka phyllosphere communities that are consistent with a dominant role of host selection in the assembly of the mānuka phyllosphere microbiome. In contrast, the phyllosphere community compositions of neighbouring, ecologically similar native plants were highly variable, suggesting that stochastic processes, such as dispersal, had a stronger influence on the phyllosphere microbiomes of those non-mānuka plants compared to the phyllosphere microbiome of mānuka. Furthermore, the distribution of phyllosphere taxa among plant species was congruent with a scenario in which microorganisms had dispersed from mānuka to non-mānuka phyllosphere microbiomes.

CONCLUSIONS

We conclude that host selection of phyllosphere communities is not and should not be presumed to be a universal trait across plant species. The specificity of the mānuka phyllosphere microbiome suggests the presence of functionally significant bacteria that are under direct, possibly chemically mediated, selection by the host. Furthermore, we propose that phyllosphere microbiomes under strong host selection, such as that of mānuka, may act as a source of microorganisms for the phyllosphere microbiomes of neighbouring plants. Video Abstract.

A salt-tolerant growth-promoting phyllosphere microbial combination from mangrove plants and its mechanism for promoting salt tolerance in rice

BACKGROUND

Mangrove plants growing in the high salt environment of coastal intertidal zones colonize a variety of microorganisms in the phyllosphere, which have potential salt-tolerant and growth-promoting effects. However, the characteristics of microbial communities in the phyllosphere of mangrove species with and without salt glands and the differences between them remain unknown, and the exploration and the agricultural utilization of functional microbial resources from the leaves of mangrove plants are insufficient.

RESULTS

In this study, we examined six typical mangrove species to unravel the differences in the diversity and structure of phyllosphere microbial communities between mangrove species with or without salt glands. Our results showed that a combination of salt-tolerant growth-promoting strains of Pantoea stewartii A and Bacillus marisflavi Y25 (A + Y25) was constructed from the phyllosphere of mangrove plants, which demonstrated an ability to modulate osmotic substances in rice and regulate the expression of salt-resistance-associated genes. Further metagenomic analysis revealed that exogenous inoculation with A + Y25 increased the rice rhizosphere's specific microbial taxon Chloroflexi, thereby elevating microbial community quorum sensing and ultimately enhancing ionic balance and overall microbial community function to aid salt resistance in rice.

CONCLUSIONS

This study advances our understanding of the mutualistic and symbiotic relationships between mangrove species and their phyllosphere microbial communities. It offers a paradigm for exploring agricultural beneficial microbial resources from mangrove leaves and providing the potential for applying the salt-tolerant bacterial consortium to enhance crop adaptability in saline-alkaline land. Video Abstract.

Amplicon Sequencing Analysis of Submerged Plant Microbiome Diversity and Screening for ACC Deaminase Production by Microbes

Submerged plants can thrive entirely underwater, playing a crucial role in maintaining water quality, supporting aquatic organisms, and enhancing sediment stability. However, they face multiple challenges, including reduced light availability, fluctuating water conditions, and limited nutrient access. Despite these stresses, submerged plants demonstrate remarkable resilience through physiological and biochemical adaptations. Additionally, their interactions with microbial communities are increasingly recognized as pivotal in mitigating these environmental stresses. Understanding the diversity of these microbial communities is crucial for comprehending the complex interactions between submerged plants and their environments. This research aims to identify and screen microbes from submerged plant samples capable of producing 1-aminocyclopropane-1-carboxylic acid (ACC) deaminase and to explore microbial diversity through metagenomic analysis. Microbes were isolated and screened for ACC deaminase production, and metagenomic techniques, including co-occurrence network analysis, were used to examine microbial diversity and interactions within the communities. ACC deaminase-producing microbes can significantly enhance plant metabolism under stress conditions. The identification of the culturable bacteria revealed that most of these microbes belong to the genera Pseudomonas, Bacillus, and Acinetobacter. A total of 177 microbial strains were cultured, with molecular identification revealing 79 reductant, 86 non-reductant, and 12 uncultured strains. Among 162 samples screened for ACC deaminase activity, 50 tested positive. To further understand microbial dynamics, samples were collected from both natural sources and artificial pond reservoirs to assess the impact of the location on flood-associated microbiomes in submerged plants. Metagenomic analysis was conducted on both the epiphytic and endophytic samples. By exploring the overall composition and dynamics of microbial communities associated with submerged plants, this research seeks to deepen our understanding of plant-microbe interactions in aquatic environments. The microbial screening helped to identify the diverse microbes associated with ACC deaminase activity in submerged plants and amplicon sequencing analysis paved the way towards identifying the impact of the location in shaping the microbiome and the diversity associated with endophytic and epiphytic microbes. Co-occurrence network analysis further highlighted the intricate interactions within these microbial communities. Notably, ACC deaminase activity was observed in plant-associated microbes across different locations, with distinct variations between epiphytic and endophytic populations as identified through co-occurrence network analysis.

Are plant traits drivers of endophytic communities in seasonally flooded tropical forests?

PREMISE

In the Amazon basin, seasonally flooded (SF) forests offer varying water constraints, providing an excellent way to investigate the role of habitat selection on microbial communities within plants. However, variations in the microbial community among host plants cannot solely be attributed to environmental factors, and how plant traits contribute to microbial assemblages remains an open question.

METHODS

We described leaf- and root-associated microbial communities using ITS2 and 16 S high-throughput sequencing and investigated the stochastic-deterministic balance shaping these community assemblies using two null models. Plant ecophysiological functioning was evaluated by focusing on 10 leaf and root traits in 72 seedlings, belonging to seven tropical SF tree species in French Guiana. We then analyzed how root and leaf traits drove the assembly of endophytic communities.

RESULTS

While both stochastic and deterministic processes governed the endophyte assembly in the leaves and roots, stochasticity prevailed. Discrepancies were found between fungi and bacteria, highlighting that these microorganisms have distinct ecological strategies within plants. Traits, especially leaf traits, host species and spatial predictors better explained diversity than composition, but they were modest predictors overall.

CONCLUSIONS

This study widens our knowledge about tree species in SF forests, a habitat sensitive to climate change, through the combined analyses of their associated microbial communities with functional traits. We emphasize the need to investigate other plant traits to better disentangle the drivers of the relationship between seedlings and their associated microbiomes, ultimately enhancing their adaptive capacities to climate change.

Grapevine bacterial communities display compartment-specific dynamics over space and time within the Central Valley of California

BACKGROUND

Plant organs (compartments) host distinct microbiota which shift in response to variation in both development and climate. Grapevines are woody perennial crops that are clonally propagated and cultivated across vast geographic areas, and as such, their microbial communities may also reflect site-specific influences. These site-specific influences along with microbial differences across sites compose 'terroir', the environmental influence on wine produced in a given region. Commercial grapevines are typically composed of a genetically distinct root (rootstock) grafted to a shoot system (scion) which adds an additional layer of complexity via genome-to-genome interactions.

RESULTS

To understand spatial and temporal patterns of bacterial diversity in grafted grapevines, we used 16S rRNA amplicon sequencing to quantify soil and compartment microbiota (berries, leaves, and roots) for grafted grapevines in commercial vineyards across three counties in the Central Valley of California over two successive growing seasons. Community composition revealed compartment-specific dynamics. Roots assembled site-specific bacterial communities that reflected rootstock genotype and environment influences, whereas bacterial communities of leaves and berries displayed associations with time.

CONCLUSIONS

These results provide further evidence of a microbial terroir within the grapevine root systems but also reveal that the microbiota of above-ground compartments are only weakly associated with the local soil microbiome in the Central Valley of California.

Relationships between Phyllosphere Bacterial Communities and Leaf Functional Traits in a Temperate Forest

As a vital component of biodiversity, phyllosphere bacteria in forest canopy play a critical role in maintaining plant health and influencing the global biogeochemical cycle. There is limited research on the community structure of phyllosphere bacteria in natural forests, which creates a gap in our understanding of whether and/or how phyllosphere bacteria are connected to leaf traits of their host. In this study, we investigated the bacterial diversity and composition of the canopy leaves of six dominant tree species in deciduous broad-leaved forests in northeastern China, using high-throughput sequencing. We then compare the differences in phyllosphere bacterial community structure and functional genes of dominant tree species. Fourteen key leaf functional traits of their host trees were also measured according to standard protocols to investigate the relationships between bacterial community composition and leaf functional traits. Our result suggested that tree species with closer evolutionary distances had similar phyllosphere microbial alpha diversity. The dominant phyla of phyllosphere bacteria were Proteobacteria, Actinobacteria, and Firmicutes. For these six tree species, the functional genes of phyllosphere bacteria were mainly involved in amino acid metabolism and carbohydrate metabolism processes. The redundancy and envfit analysis results showed that the functional traits relating to plant nutrient acquisition and resistance to diseases and pests (such as leaf area, isotope carbon content, and copper content) were the main factors influencing the community structure of phyllosphere bacteria. This study highlights the key role of plant interspecific genetic relationships and plant attributes in shaping phyllosphere bacterial diversity.

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.

Bacterial endophytes of sugar maple leaves vary more idiosyncratically than epiphytes across a large geographic area

Bacteria from the leaf surface and the leaf tissue have been attributed with several beneficial properties for their plant host. Though physically connected, the microbial ecology of these compartments has mostly been studied separately such that we lack an integrated understanding of the processes shaping their assembly. We sampled leaf epiphytes and endophytes from the same individuals of sugar maple across the northern portion of its range to evaluate if their community composition was driven by similar processes within and across populations differing in plant traits and overall abiotic environment. Leaf compartment explained most of the variation in community diversity and composition across samples. Leaf epiphytic communities were driven more by host and site characteristics than endophytic communities, whose community composition was more idiosyncratic across samples. Our results suggest a greater importance of priority effects and opportunistic colonization in driving community assembly of leaf endophytes. Understanding the comparative assembly of bacterial communities at the surface and inside plant leaves may be particularly useful for leveraging their respective potential for improving the health of plants in natural and anthropized ecosystems.

Mangroves leaves phyllosphere bacteria community and its ability to survive under pyrene stress during the acclimation process

Plants in general and mangroves in particular can harbor hyper-diverse microorganisms in their different compartments including the phyllosphere area. This study used the leaves of three mangrove species; black mangrove (Avicenia germinans), red mangrove (Rhizophora mangle) and mangrove apple (Sonneratia alba) in order to evaluate the phyllosphere epiphytic bacterial community on their leaves surface and assess the ability of some epiphytic bacteria to tolerate and survive under pyrene stress. Through the 16S rRNA genes sequencing, 380203, 405203 and 344863 OTUs were identified respectively in the leaves of mangroves apple, black and red mangroves. The identified OTUs was positively correlated with leaves-wax (p < 0.05, r² = 0.904), nitrogen (r² = 0.72), phosphorus content (r² = 0.62) and the water factor (r² = 0.93). It was however highly and negatively correlated with the canopy cover (r² = 0.93). The pyrene degradation rate in the mineral salt medium (MSM) containing pyrene as external stress was different in each mangrove species and varied depending on various factors. Therefore, through the succession culture in MSM, several bacteria strain belonging to Rhizobiales and Enterobacteres were found to be abundant in red mangroves. Bacteria belonging to Bacilliales and Sphingobacteriales were more abundant in mangroves apples and bacteria from Xanthomonadales and Sphingomonadales were more presents in back mangroves. The important finding was to reveal that the black mangrove at the non-submerged substrate, recorded the highest number of OTU, coinciding with its highest leaf's nitrogen and phosphorus content and most importantly, its highest rate of pyrene degradation. The general result of this study join previous research results and get place in the mangrove agenda, as part of a better understanding insight into the role of plant identity in driving the phyllosphere epiphytic microbial community structures in mangrove ecosystems.

Community assembly and network structure of epiphytic and endophytic phyllosphere fungi in a subtropical mangrove ecosystem

Microorganisms can influence plant growth and health, ecosystem functioning, and stability. Community and network structures of mangrove phyllosphere fungi have rarely been studied although mangroves have very important ecological and economical values. Here, we used high throughput sequencing of the internal transcribed spacer 2 (ITS2) to assess epiphytic and endophytic phyllosphere fungal communities of six true mangrove species and five mangrove associates. Totally, we obtained 1,391 fungal operational taxonomic units (OTUs), including 596 specific epiphytic fungi, 600 specific endophytic fungi, and 195 shared fungi. The richness and community composition differed significantly for epiphytes and endophytes. Phylogeny of the host plant had a significant constraint on epiphytes but not endophytes. Network analyses showed that plant–epiphyte and plant–endophyte networks exhibited strong specialization and modularity but low connectance and anti-nestedness. Compared to plant–endophyte network, plant–epiphyte network showed stronger specialization, modularity, and robustness but lower connectance and anti-nestedness. These differences in community and network structures of epiphytes and endophytes may be caused by spatial niche partitioning, indicating their underlying ecological and environmental drivers are inconsistent. We highlight the important role of plant phylogeny in the assembly of epiphytic but not endophytic fungal communities in mangrove ecosystems.

Effects of Salinity on Assembly Characteristics and Function of Microbial Communities in the Phyllosphere and Rhizosphere of Salt-Tolerant Avicennia marina Mangrove Species

It is of great significance to explore the structure and salinity response of microbial communities in salt-tolerant plants to understand the mechanisms of plant-microbe interactions. Herein, we investigated the phyllosphere and rhizosphere microbial communities of Avicennia marina, a pioneer salt-tolerant plant, at three sites with different salinities in the coastal intertidal zone. The results showed that salinity had different effects on phyllosphere and rhizosphere microbial communities and had a greater impact on bacterial communities and bacterial network interactions. The rhizosphere bacterial community alpha diversity significantly increased with increasing salinity. Moreover, the relative abundance of Proteobacteria decreased significantly, while that of Bacteroidota and Actinobacteriota, with stronger salt tolerance and nutrient utilization capacity, increased significantly. Functional prediction indicated that the microbial communities could produce catalase, peroxidase, 3-phytase, and tryptophan synthase, which may exert potential antistress and growth-promoting functions. Among them, catalase, 3-phytase, alkaline phosphatase, and acid phosphatase increased significantly in the phyllosphere and rhizosphere bacterial communities and the phyllosphere fungal community with increasing salinity. Importantly, the dominant taxa Kushneria and Bacillus, which are salt tolerant and growth promoting, were isolated from the phyllosphere and rhizosphere, respectively, and verified to have the ability to alleviate salt stress and promote the growth of rice. IMPORTANCE Avicennia marina is a pioneer salt-tolerant plant in coastal intertidal mangroves, an efficient blue carbon ecosystem. It is of great importance to explore how salinity affects the phyllosphere and rhizosphere microbial communities of A. marina. This study showed that the microbial communities in the phyllosphere and rhizosphere of A. marina had different constitutive properties, adaptive network interactions, and potential stress-promoting functions. Furthermore, the dominant bacteria Kushneria and Bacillus were obtained from the phyllosphere and rhizosphere, respectively, and their coculture with rice could effectively alleviate salt stress and promote rice growth. Additionally, the effects of salinity changes on microbial community structure, associations, and functional potential in the phyllosphere and rhizosphere of A. marina were observed. This study has enriched our understanding of the microbial community structure, function, and ecological stability of mangrove species in coastal intertidal zones and has practical significance for improving crop yield by using salt-tolerant plant microbiomes.

Compartment and Plant Identity Shape Tree Mycobiome in a Subtropical Forest

Deciphering the relationships between microbes and their host plants is critical for a better understanding of microbial diversity maintenance and community stability. Here, we investigated fungal diversity and community assembly in the phyllosphere and rhizosphere of 13 tree species in a subtropical common-garden experiment. The results showed that fungal community structures significantly differed across compartments (leaf, root, and soil) and different tree species. Higher α-diversity was observed in the phyllosphere than in the roots and rhizospheric soil. Fungal community composition (β-diversity) was significantly affected by both compartment and species identity. The fungal community compositions were significantly correlated with soil pH in the roots and the soils as well as with soil nitrate and leaf total phosphorus in the leaves. We found that fungal community assemblies were mainly driven by deterministic processes, regardless of compartments. Moreover, host preference analyses indicated that stronger plant/fungus preferences occurred in leaves than in roots and soils. Our results highlight the differences in tree mycobiome between aboveground and belowground compartments and have important implications for the promotion of biodiversity conservation and management sustainability for the subtropical forest. IMPORTANCE Subtropical mountain forests are widely distributed in Southern China and are characterized by high biodiversity. The interactions between plants and fungi play pivotal roles in biodiversity maintenance and community stability. Nevertheless, knowledge of fungal diversity and of the community assembly patterns of woody plants is scarce. Here, we investigated fungal diversity and community assembly in the phyllosphere and rhizosphere of 13 tree species in a common-garden experiment. We found that both compartment and plant identity influenced fungal diversity, community, and guild compositions, while deterministic processes mainly governed the fungal community assembly, especially in the rhizospheric fungal communities. Our results demonstrate that tree leaves represent stronger host/fungi preferences than do roots and soils. Together, our findings enhance the understanding of the roles of compartment and plant identity in structuring fungal communities as well as promote fungal diversity maintenance in subtropical mountain forest ecosystems.

Effects of shading levels on the composition and co-occurrence patterns of bacterioplankton and epibiotic bacterial communities of Cabomba caroliniana

Epibiotic bacterial community colonized on the plant leaf plays important roles in promoting plant growth and nutrient absorption, but is sensitive to environmental changes. As one of the most important environmental factors affecting the growth of plants and photosynthetic microorganisms, light may affect the diversity, composition, and interactions of the epibiotic bacterial community. Submerged plants in the aquatic ecosystem may be more sensitive to light intensity variations compared to the terrestrial plants since they usually receive less light. However, the effects of light on the interactions between the submerged plants and their epibiotic microbial communities remain uncertain. Here we used the 16S rRNA gene high-throughput sequencing to investigate the diversity and composition of the bacterioplankton and epibiotic bacterial communities of the Cabomba caroliniana under four different shading levels. A total of 24 water and leaf samples were collected from the experimental microcosms near Lake Taihu. We found the epibiotic bacterial community possessed a higher diversity than that of the bacterioplankton community, although the alpha diversity of the bacterioplankton community was more susceptible to different levels of shading. SourceTracker analysis revealed that with the increase of shading, the colonization of bacterioplankton to epibiotic bacteria decreased. Network analysis showed that the bacterial community network at 50% shading level had the lowest modularity and highest clustering coefficient compared to the bacterial community networks of other shading levels. Our findings provided new understandings of the effects of different light intensities on the epibiotic bacterial communities of submerged macrophytes.