A brief from the leaf: latest research to inform our understanding of the phyllosphere microbiome

Life on a leaf: the epiphyte to pathogen continuum and interplay in the phyllosphere

Epiphytic microbes are those that live for some or all of their life cycle on the surface of plant leaves. Leaf surfaces are a topologically complex, physicochemically heterogeneous habitat that is home to extensive, mixed communities of resident and transient inhabitants from all three domains of life. In this review, we discuss the origins of leaf surface microbes and how different biotic and abiotic factors shape their communities. We discuss the leaf surface as a habitat and microbial adaptations which allow some species to thrive there, with particular emphasis on microbes that occupy the continuum between epiphytic specialists and phytopathogens, groups which have considerable overlap in terms of adapting to the leaf surface and between which a single virulence determinant can move a microbial strain. Finally, we discuss the recent findings that the wheat pathogenic fungus Zymoseptoria tritici spends a considerable amount of time on the leaf surface, and ask what insights other epiphytic organisms might provide into this pathogen, as well as how Z. tritici might serve as a model system for investigating plant-microbe-microbe interactions on the leaf surface.

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.

Weather and leaf age separately contribute to temporal shifts in phyllosphere community structure and composition

Microbial communities living on plant leaves can positively or negatively influence plant health and, by extension, can impact whole ecosystems. Most research into the leaf microbiome consists of snapshots, and little is known about how microbial communities change over time. Weather and host physiological characteristics change over time and are often collinear with other time-varying factors, such as substrate availability, making it difficult to separate the factors driving microbial community change. We leveraged repeated measures over the course of an entire year to isolate the relative importance of environmental, host physiological, and substrate age-related factors on the assembly, structure, and composition of leaf-associated fungal communities. We applied both culturing and sequencing approaches to investigate these communities, focusing on a foundational, widely-distributed plant of conservation concern: basin big sagebrush ( Artemisia tridentata subsp. tridentata ). We found that changes in alpha diversity were independently affected by the age of a community and the air temperature. Surprisingly, total fungal abundance and species richness were not positively correlated and responded differently, sometimes oppositely, to weather. With regard to beta diversity, communities were more similar to each other across similar leaf ages, air temperatures, leaf types, and δ 13 C stable isotope ratios. Nine different genera were differentially abundant with air temperature, δ 13 C, leaf type, and leaf age, and a set of 20 genera were continuously present across the year. Our findings highlight the necessity for longer-term, repeated sampling to parse drivers of temporal change in leaf microbial communities.

Open Research Statement

All ITS DNA amplicon sequence raw data are deposited in the NCBI Sequence Read Archive (SRA), BioProject number PRJNA1107252, data will be released upon publication. All community data, metadata, taxonomic data, and R code necessary to reproduce these results are deposited in the GitHub repository archived on Zenodo: 10.5281/zenodo.11106439.

Effects of the nematode Litylenchus crenatae subsp. mccannii and beech leaf disease on leaf fungal and bacterial communities on Fagus grandifolia (American beech)

Beech leaf disease (BLD) is a newly emerging disease in North America that affects American beech (Fagus grandifolia). It is increasingly recognized that BLD is caused by a subspecies of the anguinid nematode Litylenchus crenatae subsp. mccannii (hereafter L. crenatae), which is likely native to East Asia. How nematode infestation of leaves affects the leaf microbiome and whether changes in the microbiome could contribute to BLD symptoms remain uncertain. In this study, we examined bacterial and fungal communities associated with the leaves of F. grandifolia across nine sites in Ohio and Pennsylvania that were either symptomatic or asymptomatic for BLD and used qPCR to measure relative nematode infestation levels. We found significantly higher levels of infestation at sites visibly symptomatic for BLD. Low levels of nematode infestation were also observed at asymptomatic sites, which suggests that nematodes can be present without visible symptoms evident. Bacterial and fungal communities were significantly affected by sampling site and symptomology, but only fungal communities were affected by nematode presence alone. We found many significant indicators of both bacteria and fungi related to symptoms of BLD, with taxa generally occurring in both asymptomatic and symptomatic leaves, suggesting that microbes are not responsible for BLD but could act as opportunistic pathogens. Of particular interest was the fungal genus Erysiphe, which is common in the Fagaceae and is reported to overwinter in buds-a strategy consistent with L. crenatae. The specific role microbes play in opportunistic infection of leaves affected by L. crenatae will require additional study.

IMPORTANCE

Beech leaf disease (BLD) is an emerging threat to American beech (Fagus grandifolia) and has spread quickly throughout the northeastern United States and into southern Canada. This disease leads to disfigurement of leaves and is marked by characteristic dark, interveinal banding, followed by leaf curling and drop in more advanced stages. BLD tends to especially affect understory leaves, which can lead to substantial thinning of the forest understory where F. grandifolia is a dominant tree species. Understanding the cause of BLD is necessary to employ management strategies that protect F. grandifolia and the forests where it is a foundation tree species. Current research has confirmed that the foliar nematode Litylenchus crenatae subsp. mccannii is required for BLD, but whether other organisms are involved is currently unknown. Here, we present a study that investigated leaf-associated fungi and bacteria of F. grandifolia to understand more about how microorganisms may contribute to BLD.

Disease Occurrence and Climatic Factors Jointly Structure Pomelo Leaf Fungal Succession in Disturbed Agricultural Ecosystem

For perennial plants, newly emerged organs are fresh hot spots for environmental microbes to occupy and assemble to form mature microbial communities. In the microbial community, some commensal fungi can play important roles in microbial succession, thus significantly improving host plant growth and disease resistance. However, their participating patterns in microbial assembly and succession remain largely unknown. In this study, we profiled the fungal community and found a similar fungal succession pattern of spring-emerged leaves from March to October in two pomelo orchards. Specifically, the fungal species, tracked on the old leaves, dominated the spring leaves after emergence and then decreased in relative abundance. This reduction in priority effects on the spring leaves was then followed by an increase in the number of observed species, Shannon and phylogenetic diversity indices, and the pathogen-associated fungal groups. In addition, we found that the temporal fungal succession on the spring leaves highly correlated with the disease occurrence in the orchards and with the temperature and precipitation variation from spring to summer. Of the pathogen-associated fungal groups, an increase in the relative abundance of Mycosphaerellaceae, hosting the causal agent of citrus greasy spot, correlated with the occurrence of the disease, while the relative abundance of Diaporthaceae, hosting the causal agent of melanose, was extremely low during the fungal succession. These results confirm that the two kinds of pathogen-associated fungal groups share different lifestyles on citrus, and also suggest that the study of temporal fungal succession in microbial communities can add to our understanding of the epidemiology of potential plant pathogens.

Forest top canopy bacterial communities are influenced by elevation and host tree traits

BACKGROUND

The phyllosphere microbiome is crucial for plant health and ecosystem functioning. While host species play a determining role in shaping the phyllosphere microbiome, host trees of the same species that are subjected to different environmental conditions can still exhibit large degrees of variation in their microbiome diversity and composition. Whether these intra-specific variations in phyllosphere microbiome diversity and composition can be observed over the broader expanse of forest landscapes remains unclear. In this study, we aim to assess the variation in the top canopy phyllosphere bacterial communities between and within host tree species in the temperate European forests, focusing on Fagus sylvatica (European beech) and Picea abies (Norway spruce).

RESULTS

We profiled the bacterial diversity, composition, driving factors, and discriminant taxa in the top canopy phyllosphere of 211 trees in two temperate forests, Veluwe National Parks, the Netherlands and Bavarian Forest National Park, Germany. We found the bacterial communities were primarily shaped by host species, and large variation existed within beech and spruce. While we showed that there was a core microbiome in all tree species examined, community composition varied with elevation, tree diameter at breast height, and leaf-specific traits (e.g., chlorophyll and P content). These driving factors of bacterial community composition also correlated with the relative abundance of specific bacterial families.

CONCLUSIONS

While our results underscored the importance of host species, we demonstrated a substantial range of variation in phyllosphere bacterial diversity and composition within a host species. Drivers of these variations have implications at both the individual host tree level, where the bacterial communities differed based on tree traits, and at the broader forest landscape level, where drivers like certain highly plastic leaf traits can potentially link forest canopy bacterial community variations to forest ecosystem processes. We eventually showed close associations between forest canopy phyllosphere bacterial communities and host trees exist, and the consistent patterns emerging from these associations are critical for host plant functioning.

Applied microbiology of the phyllosphere

The phyllosphere, or plant leaf surface, represents a microbial ecosystem of considerable size, holding extraordinary biodiversity and enormous potential for the discovery of new products, tools, and applications in biotechnology, agriculture, medicine, and elsewhere. This mini-review highlights the applied microbiology of the phyllosphere as an original field of study concerning itself with the genes, gene products, natural compounds, and traits that underlie phyllosphere-specific adaptations and services that have commercial and economic value for current or future innovation. Examples include plant-growth-promoting and disease-suppressive phyllobacteria, probiotics and fermented foods that support human health, as well as microbials that remedy foliar contamination with airborne pollutants, residual pesticides, or plastics. Phyllosphere microbes promote plant biomass conversion into compost, renewable energy, animal feed, or fiber. They produce foodstuffs such as thickening agents and sugar substitutes, industrial-grade biosurfactants, novel antibiotics and cancer drugs, as well as enzymes used as food additives or freezing agents. Furthermore, new developments in DNA sequence-based profiling of leaf-associated microbial communities allow for surveillance approaches in the context of food safety and security, for example, to detect enteric human pathogens on leafy greens, predict plant disease outbreaks, and intercept plant pathogens and pests on internationally traded goods. KEY POINTS: • Applied phyllosphere microbiology concerns leaf-specific adaptations for economic value • Phyllobioprospecting searches the phyllosphere microbiome for product development • Phyllobiomonitoring tracks phyllosphere microbial profiles for early risk detection.

Deep Impact: Shifts of Native Cultivable Microbial Communities on Fresh Lettuce after Treatment with Plasma-Treated Water

Foods consumed raw, such as lettuce, can host food-borne human-pathogenic bacteria. In the worst-case, these diseases cause to death. To limit illness and industrial losses, one innovative sanitation method is non-thermal plasma, which offers an extremely efficient reduction of living microbial biomass. Unfortunately, the total viable count (TVC), one of the most common methods for quantifying antimicrobial effects, provides no detailed insights into the composition of the surviving microbial community after treatment. To address this information gap, different special agars were used to investigate the reduction efficiency of plasma-treated water (PTW) on different native cultivable microorganisms. All tested cultivable microbial groups were reduced using PTW. Gram-negative bacteria showed a reduction of 3.81 log10, and Gram-positive bacteria showed a reduction of 3.49 log10. Fungi were reduced by 3.89 log10. These results were further validated using a live/dead assay. MALDI-ToF (matrix-assisted laser-desorption-ionization time-of-flight)-based determination was used for a diversified overview. The results demonstrated that Gram-negative bacteria were strongly reduced. Interestingly, Gram-positive bacteria and fungi were reduced by nearly equal amounts, but could still recover from PTW treatment. MALDI-ToF mainly identified Pseudomonas spp. and groups of Bacillus on the tested lettuce. These results indicate that the PTW treatment could efficiently achieve a ubiquitous, spectrum-wide reduction of microbial life.

Greater transmission capacities and small-world characteristics of bacterial communities in the above- than those in the below- ground niches of a typical submerged macrophyte, Vallisneria natans

Leaves and roots of submerged macrophytes provide extended surfaces and stable internal tissues for distinct microorganisms to rest, but how these microorganisms interact with each other across different niches and ultimately drive the distribution through horizontal and vertical transmissions remains largely undetermined. Knowledge of the mechanisms of assemblage and transmission in aquatic macrophytes-associated microbial communities will help to better understanding their important roles in plant fitness and benefit ecological functions. Here, we conducted a microcosmic experiment based on in situ lake samples to investigate the bacterial community assemblage, transmission, and co-occurrence patterns in different niches of a typical submerged macrophyte, Vallisneria natans (V. natans), including seed endosphere, as well as environmental (water and bulk sediment), epiphytic (phyllosphere and rhizosphere), and endophytic (leaf and root endosphere) microhabitats of both leaves and roots representatives of the above- and below- ground niches (AGNs and BGNs), respectively. We found the bacterial communities colonized in epiphytic niches not only exhibited the highest diversity compared to adjacent environmental and endophytic niches, but also dominated the interactions between those bacterial members of neighboring niches in both AGNs and BGNs. The host plants promoted niche specificity at bacterial community-level, as confirmed by the proportion of bacterial specialists increased with plant proximity, especially in the BGNs. Furthermore, the bacterial taxa colonized in the AGNs exhibited higher horizontal and vertical transmission capacities than those in the BGNs, especially in the vertical transmission from seeds to leaves (41.38 %) than roots (0.42 %). Meanwhile, the bacterial co-occurrence network in AGNs was shown to have stronger small-world characteristics but weaker stability than those in the BGNs. Overall, this study cast new light on the plant microbiome in the aquatic environment, thus better promoting the potential development of strategies for breeding aquatic macrophyte holobiont with enhanced water purification and pollutant removal capabilities in the future.

Physiological Effects of Microbial Biocontrol Agents in the Maize Phyllosphere

In a world with constant population growth, and in the context of climate change, the need to supply the demand of safe crops has stimulated an interest in ecological products that can increase agricultural productivity. This implies the use of beneficial organisms and natural products to improve crop performance and control pests and diseases, replacing chemical compounds that can affect the environment and human health. Microbial biological control agents (MBCAs) interact with pathogens directly or by inducing a physiological state of resistance in the plant. This involves several mechanisms, like interference with phytohormone pathways and priming defensive compounds. In Argentina, one of the world's main maize exporters, yield is restricted by several limitations, including foliar diseases such as common rust and northern corn leaf blight (NCLB). Here, we discuss the impact of pathogen infection on important food crops and MBCA interactions with the plant's immune system, and its biochemical indicators such as phytohormones, reactive oxygen species, phenolic compounds and lytic enzymes, focused mainly on the maize-NCLB pathosystem. MBCA could be integrated into disease management as a mechanism to improve the plant's inducible defences against foliar diseases. However, there is still much to elucidate regarding plant responses when exposed to hemibiotrophic pathogens.

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.

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.

Phagotrophic protists preserve antibiotic-resistant opportunistic human pathogens in the vegetable phyllosphere

Food safety of leafy greens is an emerging public health issue as they can harbor opportunistic human pathogens (OHPs) and expose OHPs to consumers. Protists are an integral part of phyllosphere microbial ecosystems. However, our understanding of protist-pathogen associations in the phyllosphere and their consequences on public health remains poor. Here, we examined phyllosphere protists, human pathogen marker genes (HPMGs), and protist endosymbionts from four species of leafy greens from major supermarkets in Xiamen, China. Our results showed that Staphylococcus aureus and Klebsiella pneumoniae were the dominant human pathogens in the vegetable phyllosphere. The distribution of HPMGs and protistan communities differed between vegetable species, of which Chinese chive possessed the most diverse protists and highest abundance of HPMGs. HPMGs abundance positively correlated with the diversity and relative abundance of phagotrophic protists. Whole genome sequencing further uncovered that most isolated phyllosphere protists harbored multiple OHPs which carried antibiotic resistance genes, virulence factors, and metal resistance genes and had the potential to HGT. Colpoda were identified as key phagotrophic protists which positively linked to OHPs and carried diverse resistance and virulence potential endosymbiont OHPs including Pseudomonas nitroreducens, Achromobacter xylosoxidans, and Stenotrophomonas maltophilia. We highlight that phyllosphere protists contribute to the transmission of resistant OHPs through internalization and thus pose risks to the food safety of leafy greens and human health. Our study provides insights into the protist-OHP interactions in the phyllosphere, which will help in food safety surveillance and human health.

Weather factors, soil microbiome, and bacteria-fungi interactions as drivers of the epiphytic phyllosphere communities of romaine lettuce

Lettuce is associated with seasonal outbreaks of Shiga toxin-producing Escherichia coli (STEC) infections. Little is known about how various biotic and abiotic factors affect the lettuce microbiome, which in turn impacts STEC colonization. We characterized the lettuce phyllosphere and surface soil bacterial, fungal, and oomycete communities at harvest in late-spring and -fall in California using metagenomics. Harvest season and field type, but not cultivar, significantly influenced the microbiome composition of leaves and surface soil near plants. Phyllosphere and soil microbiome compositions were correlated with specific weather factors. The relative abundance of Enterobacteriaceae, but not E. coli, was enriched on leaves (5.2%) compared to soil (0.4%) and correlated positively with minimum air temperature and wind speed. Co-occurrence networks revealed seasonal trends in fungi-bacteria interactions on leaves. These associations represented 39%-44% of the correlations between species. All significant E. coli co-occurrences with fungi were positive, while all negative associations were with bacteria. A large proportion of the leaf bacterial species was shared with those in soil, indicating microbiome transmission from the soil surface to the canopy. Our findings provide new insight into factors that shape lettuce microbial communities and the microbial context of foodborne pathogen immigration events in the lettuce phyllosphere.

Fungus-insect interactions beyond bilateral regimes: the importance and strategy to outcompete host ectomicrobiomes by fungal parasites

Fungus-insect interactions have long been investigated at the bilateral level to unveil the factors involved in mediating fungal entomopathogenicity and insect antifungal immunity. Emerging evidence has shown that insect cuticles are inhabited by different bacteria that can delay and deter fungal parasite infections. Entomopathogenic fungi (EPF), however, have evolved strategies to combat the colonization resistance mediated by insect ectomicrobiomes by producing antimicrobial peptides or antibiotic compounds. Deprivation of micronutrients may also be employed by EPF to counteract the ectomicrobiome antagonism. Further investigations of insect ectomicrobiome assemblage and fungal factors involved in outcompeting cuticular microbiomes may benefit the development of cost-effective mycoinsecticides while protecting ecologically and economically important insect species.

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.

Out of site, out of mind: Changes in feather moss phyllosphere microbiota in mine offsite boreal landscapes

Plant-microbe interactions play a crucial role in maintaining biodiversity and ecological services in boreal forest biomes. Mining for minerals, and especially the emission of heavy metal-enriched dust from mine sites, is a potential threat to biodiversity in offsite landscapes. Understanding the impacts of mining on surrounding phyllosphere microbiota is especially lacking. To investigate this, we characterized bacterial and fungal communities in the phyllosphere of feather moss Pleurozium schreberi (Brid). Mitt in boreal landscapes near six gold mine sites at different stages of the mine lifecycle. We found that (1) both mining stage and ecosystem type are drivers of the phyllosphere microbial community structure in mine offsite landscapes; (2) Bacterial alpha diversity is more sensitive than fungal alpha diversity to mining stage, while beta diversity of both groups is impacted; (3) mixed and deciduous forests have a higher alpha diversity and a distinct microbial community structure when compared to coniferous and open canopy ecosystems; (4) the strongest effects are detectable within 0.2 km from operating mines. These results confirmed the presence of offsite effects of mine sites on the phyllosphere microbiota in boreal forests, as well as identified mining stage and ecosystem type as drivers of these effects. Furthermore, the footprint was quantified at 0.2 km, providing a reference distance within which mining companies and policy makers should pay more attention during ecological assessment and for the development of mitigation strategies. Further studies are needed to assess how these offsite effects of mines affect the functioning of boreal ecosystems.

Xanthomonas infection and ozone stress distinctly influence the microbial community structure and interactions in the pepper phyllosphere

While the physiological and transcriptional response of the host to biotic and abiotic stresses have been intensely studied, little is known about the resilience of associated microbiomes and their contribution towards tolerance or response to these stresses. We evaluated the impact of elevated tropospheric ozone (O3), individually and in combination with Xanthomonas perforans infection, under open-top chamber field conditions on overall disease outcome on resistant and susceptible pepper cultivars, and their associated microbiome structure, function, and interaction network across the growing season. Pathogen infection resulted in a distinct microbial community structure and functions on the susceptible cultivar, while concurrent O3 stress did not further alter the community structure, and function. However, O3 stress exacerbated the disease severity on resistant cultivar. This altered diseased severity was accompanied by enhanced heterogeneity in associated Xanthomonas population counts, although no significant shift in overall microbiota density, microbial community structure, and function was evident. Microbial co-occurrence networks under simultaneous O3 stress and pathogen challenge indicated a shift in the most influential taxa and a less connected network, which may reflect the altered stability of interactions among community members. Increased disease severity on resistant cultivar may be explained by such altered microbial co-occurrence network, indicating the altered microbiome-associated prophylactic shield against pathogens under elevated O3. Our findings demonstrate that microbial communities respond distinctly to individual and simultaneous stressors, in this case, O3 stress and pathogen infection, and can play a significant role in predicting how plant-pathogen interactions would change in the face of climate change.

Genome Analysis of Two Pseudomonas syringae pv. aptata Strains with Different Virulence Capacity Isolated from Sugar Beet: Features of Successful Pathogenicity in the Phyllosphere Microbiome

Members of the Pseudomonas syringae species complex are heterogeneous bacteria that are the most abundant bacterial plant pathogens in the plant phyllosphere, with strong abilities to exist on and infect different plant hosts and survive in/outside agroecosystems. In this study, the draft genome sequences of two pathogenic P. syringae pv. aptata strains with different in planta virulence capacities isolated from the phyllosphere of infected sugar beet were analyzed to evaluate putative features of survival strategies and to determine the pathogenic potential of the strains. The draft genomes of P. syringae pv. aptata strains P16 and P21 are 5,974,057 bp and 6,353,752 bp in size, have GC contents of 59.03% and 58.77%, respectively, and contain 3,439 and 3,536 protein-coding sequences, respectively. For both average nucleotide identity and pangenome analysis, P16 and P21 largely clustered with other pv. aptata strains from the same isolation source. We found differences in the repertoire of effectors of the type III secretion system among all 102 selected strains, suggesting that the type III secretion system is a critical factor in the different virulent phenotypes of P. syringae pv. aptata. During genome analysis of the highly virulent strain P21, we discovered genes for T3SS effectors (AvrRpm1, HopAW1, and HopAU1) that were not previously found in genomes of P. syringae pv. aptata. We also identified coding sequences for pantothenate kinase, VapC endonuclease, phospholipase, and pectate lyase in both genomes, which may represent novel effectors of the type III secretion system. IMPORTANCE Genome analysis has an enormous effect on understanding the life strategies of plant pathogens. Comparing similarities with pathogens involved in other epidemics could elucidate the pathogen life cycle when a new outbreak happens. This study represents the first in-depth genome analysis of Pseudomonas syringae pv. aptata, the causative agent of leaf spot disease of sugar beet. Despite the increasing number of disease reports in recent years worldwide, there is still a lack of information about the genomic features, epidemiology, and pathogenic life strategies of this particular pathogen. Our findings provide advances in disease etiology (especially T3SS effector repertoire) and elucidate the role of environmental adaptations required for prevalence in the pathobiome of the sugar beet. From the perspective of the very heterogeneous P. syringae species complex, this type of analysis has specific importance in reporting the characteristics of individual strains.

Insights into the Methodological, Biotic and Abiotic Factors Influencing the Characterization of Xylem-Inhabiting Microbial Communities of Olive Trees

Vascular pathogens are the causal agents of some of the most devastating plant diseases in the world, which can cause, under specific conditions, the destruction of entire crops. These plant pathogens activate a range of physiological and immune reactions in the host plant following infection, which may trigger the proliferation of a specific microbiome to combat them by, among others, inhibiting their growth and/or competing for space. Nowadays, it has been demonstrated that the plant microbiome can be modified by transplanting specific members of the microbiome, with exciting results for the control of plant diseases. However, its practical application in agriculture for the control of vascular plant pathogens is hampered by the limited knowledge of the plant endosphere, and, in particular, of the xylem niche. In this review, we present a comprehensive overview of how research on the plant microbiome has evolved during the last decades to unravel the factors and complex interactions that affect the associated microbial communities and their surrounding environment, focusing on the microbial communities inhabiting the xylem vessels of olive trees (Olea europaea subsp. europaea), the most ancient and important woody crop in the Mediterranean Basin. For that purpose, we have highlighted the role of xylem composition and its associated microorganisms in plants by describing the methodological approaches explored to study xylem microbiota, starting from the methods used to extract xylem microbial communities to their assessment by culture-dependent and next-generation sequencing approaches. Additionally, we have categorized some of the key biotic and abiotic factors, such as the host plant niche and genotype, the environment and the infection with vascular pathogens, that can be potential determinants to critically affect olive physiology and health status in a holobiont context (host and its associated organisms). Finally, we have outlined future directions and challenges for xylem microbiome studies based on the recent advances in molecular biology, focusing on metagenomics and culturomics, and bioinformatics network analysis. A better understanding of the xylem olive microbiome will contribute to facilitate the exploration and selection of specific keystone microorganisms that can live in close association with olives under a range of environmental/agronomic conditions. These microorganisms could be ideal targets for the design of microbial consortia that can be applied by endotherapy treatments to prevent or control diseases caused by vascular pathogens or modify the physiology and growth of olive trees.

The power of light: Impact on the performance of biocontrol agents under minimal nutrient conditions

Background

The spectral distribution of light (different wavelength) has recently been identified as an important factor in the dynamics and function of leaf-associated microbes. This study investigated the impact of different wavelength on three commercial biocontrol agents (BCA): Bacillus amyloliquefaciens (BA), Pseudomonas chlororaphis (PC), and Streptomyces griseoviridis (SG).

Methods

The impact of light exposure on sole carbon source utilization, biofilm formation, and biosurfactant production by the selected BCA was studied using phenotypic microarray (PM) including 190 sole carbon sources (OmniLog®, PM panels 1 and 2). The BCA were exposed to five monochromatic light conditions (420, 460, 530, 630, and 660 nm) and darkness during incubation, at an intensity of 50 μmol m^-2 s^-1.

Results

Light exposure together with specific carbon source increased respiration in all three BCA. Different wavelengths of light influenced sole carbon utilization for the different BCA, with BA and PC showing increased respiration when exposed to wavelengths within the blue spectrum (420 and 460 nm) while respiration of selected carbon sources by SG increased in the presence of red light (630 and 660 nm). Only one carbon source (capric acid) generated biosurfactant production in all three BCA. A combination of specific wavelength of light and sole carbon source increased biofilm formation in all three BCA. BA showed significantly higher biofilm formation when exposed to blue (460 nm) and green (530 nm) light and propagated in D-sucrose, D-fructose, and dulcitol. PC showed higher biofilm formation when exposed to blue light. Biofilm formation by SG increased when exposed to red light (630 nm) and propagated in citraconic acid.

Conclusion

To increase attachment and success in BCA introduced into the phyllosphere, a suitable combination of light quality and nutrient conditions could be used.

Effects of synthetic and environmentally friendly fungicides on powdery mildew management and the phyllosphere microbiome of cucumber

Modern agricultural practices rely on synthetic fungicides to control plant disease, but the application of these fungicides has raised concerns regarding human and environmental health for many years. As a substitute, environmentally friendly fungicides have been increasingly introduced as alternatives to synthetic fungicides. However, the impact of these environmentally friendly fungicides on plant microbiomes has received limited attention. In this study, we used amplicon sequencing to compare the bacterial and fungal microbiomes in the leaves of powdery mildew-infected cucumber after the application of two environmentally friendly fungicides (neutralized phosphorous acid (NPA) and sulfur) and one synthetic fungicide (tebuconazole). The phyllosphere α-diversity of both the bacterial and fungal microbiomes showed no significant differences among the three fungicides. For phyllosphere β-diversity, the bacterial composition exhibited no significant differences among the three fungicides, but fungal composition was altered by the synthetic fungicide tebuconazole. While all three fungicides significantly reduced disease severity and the incidence of powdery mildew, NPA and sulfur had minimal impacts on the phyllosphere fungal microbiome relative to the untreated control. Tebuconazole altered the phyllosphere fungal microbiome by reducing the abundance of fungal OTUs such as Dothideomycetes and Sordariomycetes, which included potentially beneficial endophytic fungi. These results indicated that treatments with the environmentally friendly fungicides NPA and sulfur have fewer impacts on the phyllosphere fungal microbiome while maintaining the same control efficacy as the synthetic fungicide tebuconazole.

New insights into engineered plant-microbe interactions for pesticide removal

Over the past decades, rapid industrialization along with the overutilization of organic pollutants/pesticides has altered the environmental circumstances. Moreover, various anthropogenic, xenobiotics and natural activities also affected plants, soil, and human health, in both direct and indirect ways. To counter this, several conventional methods are currently practiced, but are uneconomical, noxious, and is yet inefficient for large-scale application. Plant-microbe interactions are mediated naturally in an ecosystem and are practiced in several areas. Plant growth promoting rhizobacteria (PGPR) possess certain attributes affecting plant and soil consequently performing decontamination activity via a direct and indirect mechanism. PGPR also harbors indispensable genes stimulating the mineralization of several organic and inorganic compounds. This makes microbes potential candidates for contributing to sustainably remediating the harmful pesticide contaminants. There is a limited piece of information about the plant-microbe interaction pertaining predict and understand the overall interaction concerning a sustainable environment. Therefore, this review focuses on the plant-microbe interaction in the rhizosphere and inside the plant's tissues, along with the utilization augmenting the crop productivity, reduction in plant stress along with decontamination of pesticides/organic pollutants in soil for sustainable environmental management.

Design of a biomimetic, small-scale artificial leaf surface for the study of environmental interactions

The cuticle with its superimposed epicuticular waxes represents the barrier of all aboveground parts of higher plant primary tissues. Epicuticular waxes have multiple effects on the interaction of plants with their living and non-living environment, whereby their shape, dimension, arrangement, and chemical composition play significant roles. Here, the ability of self-assembly of wax after isolation from the leaves was used to develop a small-scale wax-coated artificial leaf surface with the chemical composition and wettability of wheat (Triticum aestivum) leaves. By thermal evaporation of extracted plant waxes and adjustment of the evaporated wax amounts, the wettability and chemical character of the microstructure of the surface of wheat leaves were transferred onto a technical surface. For the use of these artificial leaves as a test system for biotic (e.g., germination of fungal pathogens) and non-biotic (e.g., applied surfactants) interactions on natural leaf surfaces, the chemical composition and the wetting behavior should be the same in both. Therefore, the morphology, chemistry, and wetting properties of natural and artificial surfaces with recrystallized wax structures were analyzed by scanning electron microscopy, gas chromatography-mass spectrometry, and by the determination of water contact angles, contact angle hysteresis, and tilting angles. Wheat leaves of different ages were covered exclusively with wax platelets. The extracted wheat wax was composed of alcohols, aldehydes, esters, and acids. The main component was 1-octacosanol. The waxes recrystallized as three-dimensional structures on the artificial surfaces. The three tested wetting parameters resembled the ones of the natural surface, providing an artificial surface with the chemical information of epicuticular waxes and the wetting properties of a natural leaf surface.

Microbial Community, Metabolic Potential and Seasonality of Endosphere Microbiota Associated with Leaves of the Bioenergy Tree Paulownia elongata × fortunei

The microbial structure and metabolic function of plant-associated endophytes play a key role in the ecology of various environments, including trees. Here, the structure and functional profiles of the endophytic bacterial community, associated with Paulownia elongata × fortunei, in correlation with seasonality, were evaluated using Biolog EcoPlates. Biolog EcoPlates was used to analyse the functional diversity of the microbiome. The total communities of leaf endophyte communities were investigated using 16S rRNA V5–V7 region amplicon deep sequencing via Illumina MiSeq. Community level physiological profiling (CLPP) analysis by the Biolog EcoPlate™ assay revealed that the carboxylic acids (19.67–36.18%) and amino acids (23.95–35.66%) were preferred by all by all communities, whereas amines and amides (0.38–9.46%) were least used. Seasonal differences in substrate use were also found. Based on the sequencing data, mainly phyla Proteobacteria (18.4–97.1%) and Actinobacteria (2.29–78.7%) were identified. A core microbiome could be found in leaf-associated endophytic communities in trees growing in different locations. This work demonstrates the application of Biolog EcoPlates in studies of the functional diversity of microbial communities in a niche other than soil and shows how it can be applied to the functional analyses of endomicrobiomes. This research can contribute to the popularisation of Biolog EcoPlates for the functional analysis of the endomicrobiome. This study confirms that the analysis of the structure and function of the plant endophytic microbiome plays a key role in the health control and the development of management strategies on bioenergy tree plantations.

A metacommunity ecology approach to understanding microbial community assembly in developing plant seeds

Microorganisms have the potential to affect plant seed germination and seedling fitness, ultimately impacting plant health and community dynamics. Because seed-associated microbiota are highly variable across individual plants, plant species, and environments, it is challenging to identify the dominant processes that underlie the assembly, composition, and influence of these communities. We propose here that metacommunity ecology provides a conceptually useful framework for studying the microbiota of developing seeds, by the application of metacommunity principles of filtering, species interactions, and dispersal at multiple scales. Many studies in seed microbial ecology already describe individual assembly processes in a pattern-based manner, such as correlating seed microbiome composition with genotype or tracking diversity metrics across treatments in dispersal limitation experiments. But we see a lot of opportunities to examine understudied aspects of seed microbiology, including trait-based research on mechanisms of filtering and dispersal at the micro-scale, the use of pollination exclusion experiments in macro-scale seed studies, and an in-depth evaluation of how these processes interact via priority effect experiments and joint species distribution modeling.

Elevated Ozone Concentration and Nitrogen Addition Increase Poplar Rust Severity by Shifting the Phyllosphere Microbial Community

Tropospheric ozone and nitrogen deposition are two major environmental pollutants. A great deal of research has focused on the negative impacts of elevated O₃ and the complementary effect of soil N addition on the physiological properties of trees. However, it has been overlooked how elevated O₃ and N addition affect tree immunity in face of pathogen infection, as well as of the important roles of phyllosphere microbiome community in host–pathogen–environment interplay. Here, we examined the effects of elevated O₃ and soil N addition on poplar leaf rust [Melampsora larici-populina] severity of two susceptible hybrid poplars [clone ‘107’: Populus euramericana cv. ‘74/76’; clone ‘546’: P. deltoides Í P. cathayana] in Free-Air-Controlled-Environment plots, in addition, the link between Mlp-susceptibility and changes in microbial community was determined using Miseq amplicon sequencing. Rust severity of clone ‘107’ significantly increased under elevated O₃ or N addition only; however, the negative impact of elevated O₃ could be significantly mitigated when accompanied by N addition, likewise, this trade-off was reflected in its phyllosphere microbial α-diversity responding to elevated O₃ and N addition. However, rust severity of clone ‘546’ did not differ significantly in the cases of elevated O₃ and N addition. Mlp infection altered microbial community composition and increased its sensitivity to elevated O₃, as determined by the markedly different abundance of taxa. Elevated O₃ and N addition reduced the complexity of microbial community, which may explain the increased severity of poplar rust. These findings suggest that poplars require a changing phyllosphere microbial associations to optimize plant immunity in response to environmental changes.

Seed inoculation with antagonistic bacteria limits occurrence of E. coli O157:H7gfp + on baby spinach leaves

Backround

During the last decades, outbreaks of foodborne illnesses have increasingly been linked to fresh and/or minimally processed fruit and vegetables. Enterohemorrhagic Escherichia coli was the causal agent for major outbreaks in Europe with leafy green vegetables and sprouts. To improve food safety, microbial antagonism has received attention during recent years and could be one of the solution to prevent contamination of food borne pathogens on fresh produce. Here we investigate the antagonistic effect of three bacterial strains (Pseudomonas orientalis, P. flavescens and Rhodococcus sp.) isolated from spinach leaves against E. coli O157:H7gfp + under laboratory and greenhouse conditions.

Results

Our results shows that significantly less culturable E.coli O157:H7gfp + were retrieved from the spinach canopy subjected to antagonist seed treatment than canopy inoculation. Seeds inoculated with Rhodococcus sp. significantly reduced growth of E. coli O157:H7gfp + compared with the other antagonists. The result from the in vitro study shows a significant reduction of growth of E. coli O157:H7gfp+, but only after 44 h when E. coli O157:H7gfp + was propagated in a mixture of spent media from all three antagonists.

Conclusions

The antagonistic effect on phyllospheric E.coli O157:H7gfp + observed after seed inoculation with Rhodococcus sp. might be an indication of induced resistance mechanism in the crop. In addition, there was a small reduction of culturable E.coli O157:H7gfp + when propagated in spent media from all three antagonists. Nutritional conditions rather than metabolites formed by the three chosen organisms appear to be critical for controlling E. coli O157:H7gfp+.

Could Bacillus biofilms enhance the effectivity of biocontrol strategies in the phyllosphere?

Maize (Zea mays L.), a major crop in Argentina and a staple food around the world, is affected by the emergence and re-emergence of foliar diseases. Agrochemicals are the main control strategy nowadays, but they can cause resistance in insects and microbial pathogens and have negative effects on the environment and human health. An emerging alternative is the use of living organisms, i.e. microbial biocontrol agents, to suppress plant pathogen populations. This is a risk-free approach when the organisms acting as biocontrol agents come from the same ecosystem as the foliar pathogens they are meant to antagonize. Some epiphytic microorganisms may form biofilm by becoming aggregated and attached to a surface, as is the case of spore-forming bacteria from the genus Bacillus. Their ability to sporulate and their tolerance to long storage periods make them a frequently used biocontrol agent. Moreover, the biofilm that they create protects them against different abiotic and biotic factors and helps them to acquire nutrients, which ensures their survival on the plants they protect. This review analyzes the interactions that the phyllosphere-inhabiting Bacillus genus establishes with its environment through biofilm, and how this lifestyle could serve to design effective biological control strategies.

Sarracenia pitcher plant-associated microbial communities differ primarily by host species across a longitudinal gradient

Plant-associated microbial communities can profoundly affect plant health and success, and research is still uncovering factors driving the assembly of these communities. Here, we examine how geography versus host species affect microbial community structure and differential abundances of individual taxa. We use metabarcoding to characterize the bacteria and eukaryotes associated with five, often co-occurring species of Sarracenia pitcher plants (Sarraceniaceae) and three natural hybrids along the longitudinal gradient of the U.S. Gulf Coast, as well as samples from S. purpurea in Massachusetts. To tease apart the effects of geography versus host species, we focus first on sites with co-occurring species and then on species located across different sites. Our analyses show that bacterial and eukaryotic community structures are clearly and consistently influenced by host species identity, with geographic factors also playing a role. Naturally-occurring hybrids appear to also host unique communities, that are in some ways intermediate between their parent species. We see significant effects of geography (site and longitude), but these generally explain less of the variation among pitcher communities. Overall, in Sarracenia pitchers, host plant phenotype significantly affects the pitcher microbiomes and other associated organisms. This article is protected by copyright. All rights reserved.

The phyllosphere microbiome shifts toward combating melanose pathogen

BACKGROUND

Plants can recruit beneficial microbes to enhance their ability to defend against pathogens. However, in contrast to the intensively studied roles of the rhizosphere microbiome in suppressing plant pathogens, the collective community-level change and effect of the phyllosphere microbiome in response to pathogen invasion remains largely elusive.

RESULTS

Here, we integrated 16S metabarcoding, shotgun metagenomics and culture-dependent methods to systematically investigate the changes in phyllosphere microbiome between infected and uninfected citrus leaves by Diaporthe citri, a fungal pathogen causing melanose disease worldwide. Multiple microbiome features suggested a shift in phyllosphere microbiome upon D. citri infection, highlighted by the marked reduction of community evenness, the emergence of large numbers of new microbes, and the intense microbial network. We also identified the microbiome features from functional perspectives in infected leaves, such as enriched microbial functions for iron competition and potential antifungal traits, and enriched microbes with beneficial genomic characteristics. Glasshouse experiments demonstrated that several bacteria associated with the microbiome shift could positively affect plant performance under D. citri challenge, with reductions in disease index ranging from 65.7 to 88.4%. Among them, Pantoea asv90 and Methylobacterium asv41 identified as "recruited new microbes" in the infected leaves, exhibited antagonistic activities to D. citri both in vitro and in vivo, including inhibition of spore germination and/or mycelium growth. Sphingomonas spp. presented beneficial genomic characteristics and were found to be the main contributor for the functional enrichment of iron complex outer membrane receptor protein in the infected leaves. Moreover, Sphingomonas asv20 showed a stronger suppression ability against D. citri in iron-deficient conditions than iron-sufficient conditions, suggesting a role of iron competition during their antagonistic action.

CONCLUSIONS

Overall, our study revealed how phyllosphere microbiomes differed between infected and uninfected citrus leaves by melanose pathogen, and identified potential mechanisms for how the observed microbiome shift might have helped plants cope with pathogen pressure. Our findings provide novel insights into understanding the roles of phyllosphere microbiome responses during pathogen challenge. Video abstract.

Diverse antibiotic resistance genes and potential pathogens inhabit in the phyllosphere of fresh vegetables

Fresh vegetables are considered as a reservoir of pathogenic bacteria and antibiotic resistance genes (ARGs), which are the emerging environmental contaminants, posing increasing concerned risk to human health. However, the prevalence of pathogens in phyllosphere of fresh vegetables, as well as the association of ARGs with pathogenic bacteria, have not been well elaborated. In this study, we explored the structure of microbial communities and ARGs through high-throughput quantitative PCR and 16S rRNA gene Illumina sequencing, and characterized the microorganisms resisting to antibiotics by pure culture. From phyllosphere of six different kinds of vegetables, 205 ARGs were detected and genes for multidrug resistance was the most abundant. The predominant potential pathogens were classified to Pseudomonas, Klebsiella, and Acinetobacter genera, which carried various ARGs such as multidrug and beta-lactam resistance genes presumedly. Among six kinds of vegetables, Lactuca sativa var. asparagina carried the highest abundance of potential pathogens and ARGs, while Allium sativum L harbored the lowest abundance of pathogens and ARGs. In addition, various culturable bacteria resisting to colistin or meropenem could be isolated from all vegetables, remarkably, all the isolates resistant to both antibiotics are potential pathogens. Our study highlighted the risks of pathogens and ARGs from raw vegetables to consumers, characterized their structure patterns among different vegetables, and analyzed the potential mechanisms regulating phyllosphere pathogens and resistome of fresh vegetables, which would be helpful for reducing the microbial risk from vegetable ingestion.

Study on the differences of phyllosphere microorganisms between poplar hybrid offspring and their parents

The females and males of dioecious plants have evolved sex-specific characteristics in terms of their morphological and physiological properties. However, the differentiation of phyllosphere microorganism of dioecious plants between parents and hybrid offspring remain largely unexplored. Here, the phyllosphere bacterial and fungal community diversity and composition of female (Populus nigra 'DH5' (PNDH5)), male (P. simonii 'DH4' (PSDH4)), and the hybrid offspring (P. simonii × P. nigra 'DH1' (PSPNDH1), P. simonii × P. nigra 'DH2' (PSPNDH2), P. simonii × P. nigra 'DH3' (PSPNDH3)) were investigated using 16S rDNA/ITS rDNA gene-based Illumina NovaSeq 6000 sequencing. There was considerable variation of plant height, diameter at breast height, leaf area, length of petioles, leaf moisture content, and starch among different samples, and PSDH2 owned the highest plant height, diameter at breast height, and length of petioles. No distinct differences of phyllosphere bacterial community diversity were observed among PSDH4, PNDH5, PSPNDH1, PSPNDH2, and PSPNDH3; while, PSPNDH2 owned the highest fungal Pielou_e index, Shannon index, and Simpson index. Firmicutes and Ascomycota were the predominant phyllosphere bacterial and fungal community at the phylum level, respectively. Bacilli and Gammaproteobacteria were the two most dominant bacterial classes regardless of parent and the hybrid offspring. The predominant phyllosphere fungal community was Dothideomycetes at the class level. The NMDS demonstrated that phyllosphere microbial community obviously differed between parents and offspring, while the phyllosphere microbial community presented some similarities under different hybrid progeny. Also, leaf characteristics contributed to the differentiation of phyllosphere bacterial and fungal communities between parents and hybrid offspring. These results highlighted the discrimination of phyllosphere microorganisms on parent and hybrid offspring, which provided clues to potential host-related species in the phyllosphere environment.

The Leaf Microbiome of Tobacco Plants across Eight Chinese Provinces

Leaf microorganism communities play significant roles in the process of plant growth, but the microbiome profiling of crop leaves is still a relatively new research area. Here, we used 16S rDNA sequencing to profile the microbiomes of 78 primary dried tobacco leaf samples from 26 locations in eight Chinese provinces. Our analyses revealed that the national leaf microbial communities contain 4473 operational taxonomic units (OTU) representing 1234 species, but there is a small, national core microbiome with only 14 OTU representing nine species. The function of this core microbiome is related to processes including nitrogen fixation, detoxification of diverse pollutants, and heavy-metal reduction. The leaf microorganism communities are obviously affected by local environments but did not exhibit obvious relationships to single ecological factors (e.g., temperature, precipitation). Our findings enhance the understanding of microbial diversity of tobacco leaves, which could be utilized for a variety of bioprocess, agricultural, and environmental detoxification applications.

Cytokinin-microbiome interactions regulate developmental functions

BACKGROUND

The interaction of plants with the complex microbial networks that inhabit them is important for plant health. While the reliance of plants on their microbial inhabitants for defense against invading pathogens is well documented, the acquisition of data concerning the relationships between plant developmental stage or aging, and microbiome assembly, is still underway. The plant hormone cytokinin (CK) regulates various plant growth and developmental processes. Here, examining the relationships between plant development and microbiome assembly, we observed developmental-age dependent changes in the phyllopshere microbiome. We show that age-related shifts in microbiome content vary based on content of, or sensitivity to, CK.

RESULTS

We found a developmental age associated decline in microbial richness and diversity, accompanied by a decline in the presence of growth promoting and resistance inducing Bacilli in the phyllosphere. This decline was absent from CK-rich or CK-hypersensitive genotypes. Bacillus isolates we obtained from CK rich genotypes were found to alter the expression of developmental genes to support morphogenesis and alter the leaf developmental program when applied to seedlings, and enhance yield and agricultural productivity when applied to mature plants.

CONCLUSIONS

Our results support the notion that CK supports developmental functions in part via the bacterial community.

It's the Economy, Stupid: Applying (Micro)economic Principles to Microbiome Science

A key challenge in microbiome science is the scale mismatch problem, which arises when the scale at which microbial communities are sampled, interrogated, and averaged is different from the scale at which individual microorganisms within those communities interact with each other and with their environment. Profiling the microbial communities in a teaspoon of soil, from a scoop of fecal matter, or along a plant leaf surface represents a scale mismatch of multiple orders of magnitude, which may limit our ability to interpret or predict species interactions and community assembly within such samples. In this Perspective, we explore how economists, who are historically and topically split along the lines of micro- and macroeconomics, deal with the scale mismatch problem, and how taking clues from (micro)economists could benefit the field of microbiomics.

Microbial Contributions for Rice Production: From Conventional Crop Management to the Use of 'Omics' Technologies

Rice, the main staple food for about half of the world's population, has had the growth of its production stagnate in the last two decades. One of the ways to further improve rice production is to enhance the associations between rice plants and the microbiome that exists around, on, and inside the plant. This article reviews recent developments in understanding how microorganisms exert positive influences on plant growth, production, and health, focusing particularly on rice. A variety of microbial species and taxa reside in the rhizosphere and the phyllosphere of plants and also have multiple roles as symbiotic endophytes while living within plant tissues and even cells. They alter the morphology of host plants, enhance their growth, health, and yield, and reduce their vulnerability to biotic and abiotic stresses. The findings of both agronomic and molecular analysis show ways in which microorganisms regulate the growth, physiological traits, and molecular signaling within rice plants. However, many significant scientific questions remain to be resolved. Advancements in high-throughput multi-omics technologies can be used to elucidate mechanisms involved in microbial-rice plant associations. Prospectively, the use of microbial inoculants and associated approaches offers some new, cost-effective, and more eco-friendly practices for increasing rice production.

Cytokinin drives assembly of the phyllosphere microbiome and promotes disease resistance through structural and chemical cues

The plant hormone cytokinin (CK) is an important developmental regulator, promoting morphogenesis and delaying differentiation and senescence. From developmental processes, to growth, to stress tolerance, CKs are central in plant life. CKs are also known to mediate plant immunity and disease resistance, and several classes of microbes can also produce CKs, affecting the interaction with their plant hosts. While host species and genotype can be a driving force in shaping the plant microbiome, how plant developmental hormones such as CK can shape the microbiome is largely uninvestigated. Here, we examined the relationship between CK and the phyllosphere microbiome, finding that CK acts as a selective force in microbiome assembly, increasing richness, and promoting the presence of Firmicutes. CK-mediated immunity was found to partially depend on the microbial community, and bacilli isolated from previously described CK-rich plant genotypes, which overexpress a CK biosynthesis gene or have increased CK sensitivity, induced plant immunity, and promoted disease resistance. Using a biomimetic system, we investigated the relationship between the leaf microstructure, which is differentially patterned upon changes in CK content or signaling, and the growth of different phyllosphere microbes. We found that leaf structures derived from CK-rich plant genotypes support bacilli in the biomimetic system. CK was able to promote the growth, swarming, and biofilm formation of immunity inducing bacillus isolates in vitro. Overall, our results indicate that host genotype and hormonal profiles can act as a strong selective force in microbiome assembly, underlying differential immunity profiles, and pathogen resistance as a result.

Characterization and Comparison of Convergence Among Cephalotus follicularis Pitcher Plant-Associated Communities With Those of Nepenthes and Sarracenia Found Worldwide

The Albany pitcher plant, Cephalotus follicularis, has evolved cup-shaped leaves and a carnivorous habit completely independently from other lineages of pitcher plants. It is the only species in the family Cephalotaceae and is restricted to a small region of Western Australia. Here, we used metabarcoding to characterize the bacterial and eukaryotic communities living in C. follicularis pitchers at two different sites. Bacterial and eukaryotic communities were correlated in both richness and composition; however, the factors associated with richness were not the same across bacteria and eukaryotes, with bacterial richness differing with fluid color, and eukaryotic richness differing with the concentration of DNA extracted from the fluid, a measure roughly related to biomass. For turnover in composition, the variation in both bacterial and eukaryotic communities primarily differed with fluid acidity, fluid color, and sampling site. We compared C. follicularis-associated community diversity with that of Australian Nepenthes mirabilis, as well as a global comparison of Southeast Asian Nepenthes and North American Sarracenia. Our results showed similarity in richness with communities from other pitcher plants, and specific bacterial taxa shared among all three independent lineages of pitcher plants. Overall, we saw convergence in richness and particular clades colonizing pitcher plants around the world, suggesting that these highly specialized habitats select for certain numbers and types of inhabitants.

Exploring the Diversity and Aromatic Hydrocarbon Degrading Potential of Epiphytic Fungi on Hornbeams from Chronically Polluted Areas

Plants can ‘catch’ and mitigate airborne pollutants and are assisted by fungi inhabiting their leaves. The structure and function of the fungal communities inhabiting the phyllosphere of hornbeam trees growing in two chronically polluted areas, the oilfield of Bóbrka and the city center of Warsaw, were compared to the ones growing in one nature reserve, the Białowieża National Park. Fungi were isolated and characterized both phylogenetically and functionally for their potential role in air pollution mitigation. Both culture-dependent (e.g., enzyme assays and tolerance tests) and culture-independent methods (e.g., ITS and shotgun sequencings) were used. Furthermore, the degradation potential of the fungi was assessed by gas chromatography mass spectrometry (GC-MS). Shotgun sequencing showed that the phyllosphere fungal communities were dominated by fungi belonging to the phylum Ascomycota. Aureobasidium was the only genus detected at the three locations with a relative abundance ≥1.0%. Among the cultivated epiphytic fungi from Bóbrka, Fusarium sporotrichioides AT11, Phoma herbarum AT15, and Lophiostoma sp. AT37 showed in vitro aromatic hydrocarbon degradation potential with laccase activities of 1.24, 3.62, and 7.2 μU L⁻¹, respectively, and peroxidase enzymes with activities of 3.46, 2.28, and 7.49 μU L⁻¹, respectively. Furthermore, Fusarium sporotrichioides AT11 and Phoma herbarum AT15 tolerated exposure to airborne naphthalene and benzene. Lophiostoma sp. AT37 was the most tolerant to exposure to these pollutants, in line with being the best potential aromatic hydrocarbon degrader isolated in this study.

Plants as a realized niche for Listeria monocytogenes

Listeria monocytogenes is a human pathogen. It is the causative agent of listeriosis, the leading cause of bacterial-linked foodborne mortality in Europe and elsewhere. Outbreaks of listeriosis have been associated with the consumption of fresh produce including vegetables and fruits. In this review we summarize current data providing direct or indirect evidence that plants can serve as habitat for L. monocytogenes, enabling this human pathogen to survive and grow. The current knowledge of the mechanisms involved in the interaction of this bacterium with plants is addressed, and whether this foodborne pathogen elicits an immune response in plants is discussed.

Microbiome-mediated effects of habitat fragmentation on native plant performance

Habitat fragmentation is a leading cause of biodiversity and ecosystem function loss in the Anthropocene. Despite the importance of plant-microbiome interactions to ecosystem productivity, we have limited knowledge of how fragmentation affects microbiomes and even less knowledge of its consequences for microbial interactions with plants. Combining field surveys, microbiome sequencing, manipulative experiments, and random forest models, we investigated fragmentation legacy effects on soil microbiomes in imperiled pine rocklands, tested how compositional shifts across 14 fragmentation-altered soil microbiomes affected performance and resource allocation of three native plant species, and identified fragmentation-responding microbial families underpinning plant performance. Legacies of habitat fragmentation were associated with significant changes in microbial diversity and composition (across three of four community axes). Experiments showed plants often strongly benefited from the microbiome's presence, but fragmentation-associated changes in microbiome composition also significantly affected plant performance and resource allocation across all seven metrics examined. Finally, random forest models identified ten fungal and six bacterial families important for plant performance that changed significantly with fragmentation. Our findings not only support the existence of significant fragmentation effects on natural microbiomes, but also demonstrate for the first time that fragmentation-associated changes in microbiomes can have meaningful consequences for native plant performance and investment.

Biochemical and Metabolic Plant Responses toward Polycyclic Aromatic Hydrocarbons and Heavy Metals Present in Atmospheric Pollution

Heavy metals (HMs) and polycyclic aromatic hydrocarbons (PAHs) are toxic components of atmospheric particles. These pollutants induce a wide variety of responses in plants, leading to tolerance or toxicity. Their effects on plants depend on many different environmental conditions, not only the type and concentration of contaminant, temperature or soil pH, but also on the physiological or genetic status of the plant. The main detoxification process in plants is the accumulation of the contaminant in vacuoles or cell walls. PAHs are normally transformed by enzymatic plant machinery prior to conjugation and immobilization; heavy metals are frequently chelated by some molecules, with glutathione, phytochelatins and metallothioneins being the main players in heavy metal detoxification. Besides these detoxification mechanisms, the presence of contaminants leads to the production of the reactive oxygen species (ROS) and the dynamic of ROS production and detoxification renders different outcomes in different scenarios, from cellular death to the induction of stress resistances. ROS responses have been extensively studied; the complexity of the ROS response and the subsequent cascade of effects on phytohormones and metabolic changes, which depend on local concentrations in different organelles and on the lifetime of each ROS species, allow the plant to modulate its responses to different environmental clues. Basic knowledge of plant responses toward pollutants is key to improving phytoremediation technologies.

Phyllosphere microbiome: Diversity and functions

Phyllosphere or aerial surface of plants represents the globally largest and peculiar microbial habitat that inhabits diverse and rich communities of bacteria, fungi, viruses, cyanobacteria, actinobacteria, nematodes, and protozoans. These hyperdiverse microbial communities are related to the host's specific functional traits and influence the host's physiology and the ecosystem's functioning. In the last few years, significant advances have been made in unravelling several aspects of phyllosphere microbiology, including diversity and microbial community composition, dynamics, and functional interactions. This review highlights the current knowledge about the assembly, structure, and composition of phyllosphere microbial communities across spatio-temporal scales, besides functional significance of different microbial communities to the plant host and the surrounding environment. The knowledge will help develop strategies for modelling and manipulating these highly beneficial microbial consortia for furthering scientific inquiry into their interactions with the host plants and also for their useful and economic utilization.

Fungal diversity within the phyllosphere of Pinus massoniana and the possible involvement of phyllospheric fungi in litter decomposition

Fungi play key roles in forest ecosystems and help to shape the forest's diverse functions. However, little is known about the diversity of phyllospheric fungi or their possible relationships with fungal communities residing in different micro-environments of Pinus massoniana forests. We investigated seven different sample types: mature needles (NM), dead needles (ND), needles falling as litter (L), fermenting needles (F), humus (H), top soil (0-20 cm) (TS), and secondary soil (20-40 cm) (SS). These seven fungal communities were examined and compared with ITS amplicons using a high-throughput sequencing technique. A total of 1213 fungal operational taxonomic units (OTUs) were obtained at a 97% sequence similarity level. Distinct fungal communities were associated with different sample types. A greater number of OTUs were present in both NM and F samples than those shared by both NM and TS samples, indicating that phyllospheric fungi may play crucial roles in litter decomposition. Sixty OTUs (the core microbiome) were found in all sample types, and they may probably play different ecological roles in different sample types. These findings extend our knowledge of the fungal diversity of the phyllosphere and its possible interactions with fungal communities found in distinct forest micro-habitats.

Home-field advantage of litter decomposition: from the phyllosphere to the soil

Plants often associate with specialized decomposer communities that increase plant litter breakdown, a phenomenon that is known as the 'home-field advantage' (HFA). Although the concept of HFA has long considered only the role of the soil microbial community, explicit consideration of the role of the microbial community on the foliage before litter fall (i.e. the phyllosphere community) may help us to better understand HFA. We investigated the occurrence of HFA in the presence vs absence of phyllosphere communities and found that HFA effects were smaller when phyllosphere communities were removed. We propose that priority effects and interactions between phyllosphere and soil organisms can help explain the positive effects of the phyllosphere at home, and suggest a path forward for further investigation.

Extension of Plant Phenotypes by the Foliar Microbiome

The foliar microbiome can extend the host plant phenotype by expanding its genomic and metabolic capabilities. Despite increasing recognition of the importance of the foliar microbiome for plant fitness, stress physiology, and yield, the diversity, function, and contribution of foliar microbiomes to plant phenotypic traits remain largely elusive. The recent adoption of high-throughput technologies is helping to unravel the diversityand spatiotemporal dynamics of foliar microbiomes, but we have yet to resolve their functional importance for plant growth, development, and ecology. Here, we focus on the processes that govern the assembly of the foliar microbiome and the potential mechanisms involved in extended plant phenotypes. We highlight knowledge gaps and provide suggestions for new research directions that can propel the field forward. These efforts will be instrumental in maximizing the functional potential of the foliar microbiome for sustainable crop production.

Beyond the Wall: Exopolysaccharides in the Biofilm Lifestyle of Pathogenic and Beneficial Plant-Associated Pseudomonas

The formation of biofilms results from a multicellular mode of growth, in which bacteria remain enwrapped by an extracellular matrix of their own production. Many different bacteria form biofilms, but among the most studied species are those that belong to the Pseudomonas genus due to the metabolic versatility, ubiquity, and ecological significance of members of this group of microorganisms. Within the Pseudomonas genus, biofilm studies have mainly focused on the opportunistic human pathogen Pseudomonas aeruginosa due to its clinical importance. The extracellular matrix of P. aeruginosa is mainly composed of exopolysaccharides, which have been shown to be important for the biofilm architecture and pathogenic features of this bacterium. Notably, some of the exopolysaccharides recurrently used by P. aeruginosa during biofilm formation, such as the alginate and polysaccharide synthesis loci (Psl) polysaccharides, are also used by pathogenic and beneficial plant-associated Pseudomonas during their interaction with plants. Interestingly, their functions are multifaceted and seem to be highly dependent on the bacterial lifestyle and genetic context of production. This paper reviews the functions and significance of the exopolysaccharides produced by plant-associated Pseudomonas, particularly the alginate, Psl, and cellulose polysaccharides, focusing on their equivalents produced in P. aeruginosa within the context of pathogenic and beneficial interactions.