Both leaf properties and microbe-microbe interactions influence within-species variation in bacterial population diversity and structure in the lettuce (Lactuca Species) phyllosphere

Growth period and variety together drive the succession of phyllosphere microbial communities of grapevine

Phyllosphere microbes play a crucial role in plant health and productivity. However, the influence of abiotic and biotic factors on these communities is poorly understood. Here, we used amplicon sequencing to investigate the microbiome variations across eight grape cultivars and three distinct leaf ages. The diversity and richness of phyllosphere microbiomes were significantly affected by cultivars and leaf age. Young leaves of most grape cultivars had a higher diversity. Beta-diversity analyses revealed notable differences in microbial communities across leaf ages, with bacterial communities varying substantially between cultivars. The main bacterial genera included Staphylococcus, Exiguobacterium, Acinetobacter, Enterococcus, and Erwinia; the principal fungal genera were Cladosporium, Moesziomyces, Alternaria, Didymella, and Coprinellus across all samples. LEfSe analysis revealed significant differences in bacterial and fungal biomarkers at different leaf ages, with no biomarkers identified among different cultivars. Fungal biomarkers were more abundant than bacterial at three leaf ages, and older leaves had more fungal biomarkers. Notably, beneficial microbial taxa with biocontrol potential were present on the phyllosphere at 45 d, whereas certain fungal groups associated with increased disease risk were first detected at 100 d. The bacterial network was more complex than the fungal network, and young leaves had a more complex network in most cultivars. Our study elucidated the dynamics of early grape phyllosphere microbes, providing valuable insights for early detection and prediction of grape diseases and a foundation for leveraging the grape leaf microbiome for agricultural purposes.

Exploring the diversity and potential functional characteristics of microbiota associated with different compartments of Schisandra chinensis

Introduction

Symbiotic microbial have a significant impact on the growth and metabolism of medicinal plants. Schisandra chinensis is a very functionally rich medicinal herb; however, its microbial composition and diversity have been poorly studied.

Methods

In the present study, the core microbiomes associated with the rhizospheric soil, roots, stems, leaves, and fruits of S. chinensis from six geographic locations were analyzed by a macro-genomics approach.

Results

Alpha and beta diversity analyses showed that the diversity of microbial composition of S. chinensis fruits did not differ significantly among the geographic locations as compared to that in different plant compartments. Principal coordinate analysis showed that the microbial communities of S. chinensis fruits from the different ecological locations were both similar and independent. In all S. chinensis samples, Proteobacteria was the most dominant bacterial phylum, and Ascomycota and Basidiomycota were the most dominant fungal phyla. Nitrospira, Bradyrhizobium, Sphingomonas, and Pseudomonas were the marker bacterial populations in rhizospheric soils, roots, stems and leaves, and fruits, respectively, and Penicillium, Golubevia, and Cladosporium were the marker fungal populations in the rhizospheric soil and roots, stems and leaves, and fruits, respectively. Functional analyses showed a high abundance of the microbiota mainly in biosynthesis.

Discussion

The present study determined the fungal structure of the symbiotic microbiome of S. chinensis, which is crucial for improving the yield and quality of S. chinensis.

Leaf surface microbiota transplantation confers resistance to coffee leaf rust in susceptible Coffea arabica

Coffee leaf rust, caused by the fungus Hemileia vastatrix, has become a major concern for coffee-producing countries. Additionally, there has been an increase in the resistance of certain races of the fungus to fungicides and breeding cultivars, making producers use alternative control methods. In this work, we transplanted the leaf surface microbiota of rust-resistant coffee species (Coffea racemosa and Coffea stenophylla) to Coffea arabica and tested whether the new microbiota would be able to minimize the damage caused by H. vastatrix. It was seen that the transplant was successful in controlling rust, especially from C. stenophylla, but the protection depended on the concentration of the microbiota. Certain fungi, such as Acrocalymma, Bipolaris, Didymella, Nigrospora, Setophaeosphaeria, Simplicillium, Stagonospora and Torula, and bacteria, such as Chryseobacterium, Sphingobium and especially Enterobacter, had their populations increased and this may be related to the antagonism seen against H. vastatrix. Interestingly, the relative population of bacteria from genera Pantoea, Methylobacterium and Sphingomonas decreased after transplantation, suggesting a positive interaction between them and H. vastatrix development. Our findings may help to better understand the role of the microbiota in coffee leaf rust, as well as help to optimize the development of biocontrol agents.

Characteristics of the phyllosphere microbial community and its relationship with major aroma precursors during the tobacco maturation process

Numerous bacteria, fungi and other microorganisms in the tobacco phyllosphere interstellar area participate in the physiological metabolism of plants by interacting with the host. However, there is currently little research on the characteristics of tobacco phyllosphere microbial communities, and the correlation between tobacco phyllosphere microbial communities and phyllosphere factor indicators is still unknown. Therefore, high-throughput sequencing technology based on the 16S rRNA/ITS1 gene was used to explore the diversity and composition characteristics of tobacco phyllosphere bacterial and fungal communities from different maturation processes, and to identify marker genera that distinguish phyllosphere microbial communities. In this study, the correlations between tobacco phyllosphere bacterial and fungal communities and the precursors of major aroma compounds were explored. The results showed that as the tobacco plants matured, the density of glandular trichomes on the tobacco leaves gradually decreased. The surface physicochemical properties of tobacco leaves also undergo significant changes. In addition, the overall bacterial alpha diversity in the tobacco phyllosphere area increased with maturation, while the overall fungal alpha diversity decreased. The beta diversity of bacteria and fungi in the tobacco phyllosphere area also showed significant differences. Specifically, with later top pruning time, the relative abundances of Acidisoma, Ralstonia, Bradyrhizobium, Alternaria and Talaromyces gradually increased, while the relative abundances of Pseudomonas, Filobassidium, and Tausonia gradually decreased. In the bacterial community, Acidisoma, Ralstonia, Bradyrhizobium, and Alternaria were significantly positively correlated with tobacco aroma precursors, with significant negative correlations with tobacco phyllosphere trichome morphology, while Pseudomonas showed the opposite pattern; In the fungal community, Filobasidium and Tausonia were significantly negatively correlated with tobacco aroma precursors, and significantly positively correlated with tobacco phyllosphere trichome morphology, while Alternaria showed the opposite pattern. In conclusion, the microbiota (bacteria and fungi) and aroma precursors of the tobacco phyllosphere change significantly as tobacco matures. The presence of Acidisoma, Ralstonia, Bradyrhizobium and Alternaria in the phyllosphere microbiota of tobacco may be related to the aroma precursors of tobacco.

Minimizing Escherichia coli O157:H7 contamination in indoor farming: effects of cultivar type and ultra-violet light quality

BACKGROUND

Bacterial contamination of produce is a concern in indoor farming due to close plant spacing, recycling irrigation, warm temperatures, and high relative humidity during production. Cultivars that inherently resist contamination and photo-sanitization using ultraviolet (UV) radiation during the production phase can reduce bacterial contamination. However, there is limited information to support their use in indoor farming.

RESULTS

Lettuce (Lactuca sativa) cultivars with varying plant architectures grown in a custom-built indoor farm exhibited differences in E. coli O157:H7 survival after inoculation. The survival of E. coli O157:H7 was lowest in the leaf cultivar (open architecture) and highest in the romaine and oakleaf cultivars (compact architecture). Of the different UV wavelengths that were tested (UV-A, UV-A + B, UV-A + C), UV A + C at an intensity of 54.5 μmol m-2 s-1 (with 3.5 μmol m-2 s-1 of UV-C), provided for 15 min every day, was found to be most efficacious in reducing the E. coli O157:H7 survival on romaine lettuce with no negative effects on plant growth and quality.

CONCLUSION

Contamination of E. coli O157:H7 on lettuce plants can be reduced and the food safety levels in indoor farms can be increased by selecting cultivars with an open leaf architecture coupled with photo-sanitization using low and frequent exposure to UV A + C radiation. © 2024 The Authors. Journal of The Science of Food and Agriculture published by John Wiley & Sons Ltd on behalf of Society of Chemical Industry.

Transfer of Salmonella, Escherichia coli O157:H7 and Listeria monocytogenes from contaminated soilless substrate and seeds to microgreens

Microgreens can be contaminated by various preharvest sources including soilless substrate, plant nutrition solution, water and seeds. The aim of this study was to determine the transfer level of Salmonella, Shiga toxin-producing Escherichia coli O157:H7, and Listeria monocytogenes to the edible part of various type of microgreens from plant nutrient solution-soaked perlite as soilless substrate or seeds. Ampicillin resistant 3-strain cocktails of Salmonella and E. coli O157:H7 and non-resistant L. monocytogenes were independently inoculated into plant nutrient solution-soaked perlite and seeds in low (102-103 CFU/g) and high (105-106 CFU/g) populations. Twenty types of microgreens were grown in inoculated perlite. The seed inoculation was performed on five types of microgreens. Correlations between pathogen transfer levels with seed characteristics and harvest time were assessed. Pathogen populations (1.6 ± 0.2 to 7.7 ± 0.1 log CFU/g) transferred to microgreens were dependent on type of pathogen and microgreen but not affected by contamination source and inoculation level. The level of pathogen transferred to microgreens had a moderate to high negative correlations (R2) with seed surface area (-0.551 to -0.781), seed weight (-0.735 to -0.818), and harvest time (-0.332 to -0.919) when grown in Salmonella and E. coli O157:H7 inoculated perlite. This study suggests a high risk of pathogen population transferring to microgreens in case of seed or soilless substrate contamination when pathogen growth or survival is supported in plant nutrient solution.

Interplay between Amaryllidaceae alkaloids, the bacteriome and phytopathogens in Lycoris radiata

Alkaloids are a large group of plant secondary metabolites with various structures and activities. It is important to understand their functions in the interplay between plants and the beneficial and pathogenic microbiota. Amaryllidaceae alkaloids (AAs) are unique secondary metabolites in Amaryllidaceae plants. Here, we studied the interplay between AAs and the bacteriome in Lycoris radiata, a traditional Chinese medicinal plant containing high amounts of AAs. The relationship between AAs and bacterial composition in different tissues of L. radiata was studied. In vitro experiments revealed that AAs have varying levels of antimicrobial activity against endophytic bacteria and pathogenic fungi, indicating the importance of AA synthesis in maintaining a balance between plants and beneficial/pathogenic microbiota. Using bacterial synthetic communities with different compositions, we observed a positive feedback loop between bacteria insensitive to AAs and their ability to increase accumulation of AAs in L. radiata, especially in leaves. This may allow insensitive bacteria to outcompete sensitive ones for plant resources. Moreover, the accumulation of AAs enhanced by insensitive bacteria could benefit plants when challenged with fungal pathogens. This study highlights the functions of alkaloids in plant-microbe interactions, opening new avenues for designing plant microbiomes that could contribute to sustainable agriculture.

Light Intensity Modulates the Functional Composition of Leaf Metabolite Groups and Phyllosphere Prokaryotic Community in Garden Lettuce (Lactuca sativa L.) Plants at the Vegetative Stage

Light intensity primarily drives plant growth and morphogenesis, whereas the ecological impact of light intensity on the phyllosphere (leaf surface and endosphere) microbiome is poorly understood. In this study, garden lettuce (Lactuca sativa L.) plants were grown under low, medium, and high light intensities. High light intensity remarkably induced the leaf contents of soluble proteins and chlorophylls, whereas it reduced the contents of leaf nitrate. In comparison, medium light intensity exhibited the highest contents of soluble sugar, cellulose, and free amino acids. Meanwhile, light intensity resulted in significant changes in the composition of functional genes but not in the taxonomic compositions of the prokaryotic community (bacteria and archaea) in the phyllosphere. Notably, garden lettuce plants under high light intensity treatment harbored more sulfur-cycling mdh and carbon-cycling glyA genes than under low light intensity, both of which were among the 20 most abundant prokaryotic genes in the leaf phyllosphere. Furthermore, the correlations between prokaryotic functional genes and lettuce leaf metabolite groups were examined to disclose their interactions under varying light intensities. The relative abundance of the mdh gene was positively correlated with leaf total chlorophyll content but negatively correlated with leaf nitrate content. In comparison, the relative abundance of the glyA gene was positively correlated with leaf total chlorophyll and carotenoids. Overall, this study revealed that the functional composition of the phyllosphere prokaryotic community and leaf metabolite groups were tightly linked in response to changing light intensities. These findings provided novel insights into the interactions between plants and prokaryotic microbes in indoor farming systems, which will help optimize environmental management in indoor farms and harness beneficial plant-microbe relationships for crop production.

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.

The Changes of Phyllosphere Fungal Communities among Three Different Populus spp

As an ecological index for plants, the diversity and structure of phyllosphere microbial communities play a crucial role in maintaining ecosystem stability and balance; they can affect plant biogeography and ecosystem function by influencing host fitness and function. The phyllosphere microbial communities reflect the immigration, survival, and growth of microbial colonists, which are influenced by various environmental factors and leaves' physical and chemical properties. This study investigated the structure and diversity of phyllosphere fungal communities in three different Populus spp., namely-P. × euramaricana (BF3), P. nigra (N46), and P. alba × P. glandulosa (84K). Leaves' chemical properties were also analyzed to identify the dominant factors affecting the phyllosphere fungal communities. N46 exhibited the highest contents of total nitrogen (Nt), total phosphorus (Pt), soluble sugar, and starch. Additionally, there were significant variations in the abundance, diversity, and composition of phyllosphere fungal communities among the three species: N46 had the highest Chao1 index and observed_species, while 84K had the highest Pielou_e index and Simpson index. Ascomycota and Basidiomycota are the dominant fungal communities at the phylum level. Results from typical correlation analyses indicate that the chemical properties of leaves, especially total phosphorus (Pt), total nitrogen (Nt), and starch content, significantly impact the structure and diversity of the phyllosphere microbial community. However, it is worth noting that even under the same stand conditions, plants from different species have distinct leaf characteristics, proving that the identity of the host species is the critical factor affecting the structure of the phyllosphere fungal community.

Co-evolution within the plant holobiont drives host performance

Plants interact with a diversity of microorganisms that influence their growth and resilience, and they can therefore be considered as ecological entities, namely "plant holobionts," rather than as singular organisms. In a plant holobiont, the assembly of above- and belowground microbiota is ruled by host, microbial, and environmental factors. Upon microorganism perception, plants activate immune signaling resulting in the secretion of factors that modulate microbiota composition. Additionally, metabolic interdependencies and antagonism between microbes are driving forces for community assemblies. We argue that complex plant-microbe and intermicrobial interactions have been selected for during evolution and may promote the survival and fitness of plants and their associated microorganisms as holobionts. As part of this process, plants evolved metabolite-mediated strategies to selectively recruit beneficial microorganisms in their microbiota. Some of these microbiota members show host-adaptation, from which mutualism may rapidly arise. In the holobiont, microbiota members also co-evolved antagonistic activities that restrict proliferation of microbes with high pathogenic potential and can therefore prevent disease development. Co-evolution within holobionts thus ultimately drives plant performance.

Characterization of endophytic bacteriome diversity and associated beneficial bacteria inhabiting a macrophyte Eichhornia crassipes

Introduction

The endosphere of a plant is an interface containing a thriving community of endobacteria that can affect plant growth and potential for bioremediation. Eichhornia crassipes is an aquatic macrophyte, adapted to estuarine and freshwater ecosystems, which harbors a diverse bacterial community. Despite this, we currently lack a predictive understanding of how E. crassipes taxonomically structure the endobacterial community assemblies across distinct habitats (root, stem, and leaf).

Methods

In the present study, we assessed the endophytic bacteriome from different compartments using 16S rRNA gene sequencing analysis and verified the in vitro plant beneficial potential of isolated bacterial endophytes of E. crassipes.

Results and discussion

Plant compartments displayed a significant impact on the endobacterial community structures. Stem and leaf tissues were more selective, and the community exhibited a lower richness and diversity than root tissue. The taxonomic analysis of operational taxonomic units (OTUs) showed that the major phyla belonged to Proteobacteria and Actinobacteriota (> 80% in total). The most abundant genera in the sampled endosphere was Delftia in both stem and leaf samples. Members of the family Rhizobiaceae, such as in both stem and leaf samples. Members of the family Rhizobiaceae, such as Allorhizobium- Neorhizobium-Pararhizobium-Rhizobium were mainly associated with leaf tissue, whereas the genera Nannocystis and Nitrospira from the families Nannocystaceae and Nitrospiraceae, respectively, were statistically significantly associated with root tissue. Piscinibacter and Steroidobacter were putative keystone taxa of stem tissue. Most of the endophytic bacteria isolated from E. crassipes showed in vitro plant beneficial effects known to stimulate plant growth and induce plant resistance to stresses. This study provides new insights into the distribution and interaction of endobacteria across different compartments of E. crassipes Future study of endobacterial communities, using both culture-dependent and -independent techniques, will explore the mechanisms underlying the wide-spread adaptability of E. crassipesto various ecosystems and contribute to the development of efficient bacterial consortia for bioremediation and plant growth promotion.

Commonly Consumed Vegetables as a Potential Source of Multidrug-Resistant and β-Lactamase-Producing Bacteria in Debre Berhan Town, Ethiopia

Background

Recently, antibiotic resistance of bacteria contained in foods such as vegetables has become a public health problem. In Ethiopia, the diversity of bacterial contamination and level of antibiotic resistance in vegetables are poorly understood. Local analysis of vegetable contamination and its contribution to the spread of antibiotic resistance are therefore essential for One Health interventions. Therefore, the aim of this study was to investigate the level of bacterial contamination of commonly consumed vegetables and their antimicrobial resistance patterns.

Methods

A cross-sectional research was conducted in Debre Berhan town from February to August 2022. Questionnaires were used to collect data on sociodemographic variables, hygiene practices, and market hygiene. Six carefully selected vegetables (30 each, 180 in total) were purchased at a local market. Bacterial isolation and identification, multidrug-resistant (MDR) screening and confirmation, extended-spectrum β-lactamase (ESBL) screening and confirmation, and antibiotic susceptibility tests were performed using standard operating procedure. The data were analysed statistically using SPSS software version 25.

Results

The contamination rate of vegetables was 119 (66.1%). Of the 176 bacteria isolates, E. coli (26.1%; 46/176), S. aureus (18.8%; 176), S. epidermidis (10.8%; 19/176), Klebsiella spp. (9.1%; 16/179) and Acinetobacter spp. (6.8%; 12/176) were the most frequently detected isolates. Of the 180 samples tested, (66.1%; 119/180) were contaminated with at least one type of bacteria. Lettuce (22.7%; 40/176), spinach (18.6%; 33/176), and cabbage (19.2%; 32/176) were the most contaminated vegetables. Of the 176 bacteria isolates, (64.8%; 114/176) were MDR, and (18.5%; 23/124) isolates were ESBL producers. The kind of vegetables, vendor/seller finger-nail status, medium of display, market type, and not cleaned before to display were all significantly associated with bacterial contamination.

Conclusion

This study found that commonly consumed vegetables are contaminated with antibiotic-resistant bacteria. Vegetables were also notable for the incidence of multidrug-resistant, extended β-lactamase-resistant, and methicillin-resistant bacterial isolates. Therefore, we urge local health authorities to develop and implement effective control strategies to reduce vegetable contamination.

The mature phyllosphere microbiome of grapevine is associated with resistance against Plasmopara viticola

Phyllosphere microbiota represents a substantial but hardly explored reservoir for disease resistance mechanisms. The goal of our study was to understand the link between grapevine cultivars susceptibility to Plasmopara viticola, one of the most devastating leaf pathogens in viticulture, and the phyllosphere microbiota. Therefore, we analyzed a 16S rRNA gene library for the dominant phyllosphere bacterial phyla Alphaproteobacteria of seven Vitis genotypes at different developmental stages, i.e., flowering and harvesting, via amplicon sequencing. Young leaves had significantly higher Alphaproteobacterial richness and diversity without significant host-specificity. In contrast, the microbial communities of mature leaves were structurally distinct in accordance with P. viticola resistance levels. This statistically significant link between mature bacterial phyllosphere communities and resistant phenotypes was corroborated by beta diversity metrics and network analysis. Beyond direct host-driven effects via the provision of microhabitats, we found evidence that plants recruit for specific bacterial taxa that were likely playing a fundamental role in mediating microbe-microbe interactions and structuring clusters within mature communities. Our results on grape-microbiota interaction provide insights for targeted biocontrol and breeding strategies.

Differences in phyllosphere microbiomes among different Populus spp. in the same habitat

INTRODUCTION

The above-ground parts of terrestrial plants are collectively known as the phyllosphere. The surface of the leaf blade is a unique and extensive habitat for microbial communities. Phyllosphere bacteria are the second most closely associated microbial group with plants after fungi and viruses, and are the most abundant, occupying a dominant position in the phyllosphere microbial community. Host species are a major factor influencing the community diversity and structure of phyllosphere microorganisms.

METHODS

In this study, six Populus spp. were selected for study under the same site conditions and their phyllosphere bacterial community DNA fragments were paired-end sequenced using 16S ribosomal RNA (rRNA) gene amplicon sequencing. Based on the distribution of the amplicon sequence variants (ASVs), we assessed the alpha-diversity level of each sample and further measured the differences in species abundance composition among the samples, and predicted the metabolic function of the community based on the gene sequencing results.

RESULTS

The results revealed that different Populus spp. under the same stand conditions resulted in different phyllosphere bacterial communities. The bacterial community structure was mainly affected by the carbon and soluble sugar content of the leaves, and the leaf nitrogen, phosphorus and carbon/nitrogen were the main factors affecting the relative abundance of phyllosphere bacteria.

DISCUSSION

Previous studies have shown that a large proportion of the variation in the composition of phyllosphere microbial communities was explained by the hosts themselves. In contrast, leaf-borne nutrients were an available resource for bacteria living on the leaf surface, thus influencing the community structure of phyllosphere bacteria. These were similar to the conclusions obtained in this study. This study provides theoretical support for the study of the composition and structure of phyllosphere bacterial communities in woody plants and the factors influencing them.

Natural variation and drought-induced differences in metabolite profiles of red oak-leaf and Romaine lettuce play a role in modulating the interaction with Salmonella enterica

Nutrients on produce surfaces are vital for successful enteric pathogen colonisation. In this study, we investigated natural variation in metabolite profiles of Romaine 'Parris Island Cos' and red oak-leaf lettuce 'Mascara' under regular and restricted watering conditions. We also investigated the impact of plant drought stress on the Salmonella - lettuce association. Salmonella Newport and Typhimurium were able to persist at higher levels on regularly watered Romaine than red oak-leaf lettuce. Drought treatment to lettuce impaired epiphytic Salmonella association, with S. Newport and Typhimurium being differentially affected. A higher log reduction of both serotypes was measured on drought-subjected red oak-leaf lettuce plants than controls, but S. Typhimurium was unaffected on water deficit-treated Romaine lettuce (p < 0.05). To assess Salmonella interaction with leaf surface metabolites, leaf washes collected from both cultivars were inoculated and found to be able to support S. Newport growth, with higher levels of Salmonella retrieved from Romaine washes (p < 0.05). The lag phase of S. Newport in washes from water restricted red oak-leaf lettuce was prolonged in relation to regularly-watered controls (p < 0.05). Untargeted plant metabolite profiling using electrospray ionization time-of-flight mass spectrometry (ESI-TOF-MS) revealed natural variation between Romaine and red oak-leaf lettuce profiles for leaf tissue and leaf washes. Metabolite profile shifts were detected in both lettuce types in response to drought stress, but more unique peaks were detected in red oak-leaf than Romaine lettuce after drought treatment. Variation between the two cultivars was in part attributed to naturally higher levels of flavonoids and anthocyanins in red oak-leaf lettuce compared to Romaine. Moreover, red oak-leaf, but not Romaine lettuce, responded to drought by inducing the accumulation of proline, phenolics, flavonoids and anthocyanins. Drought stress, therefore, enhanced the functional food properties of red oak-leaf lettuce. Salmonella growth dynamics in lettuce leaf washes suggested that natural variation and drought-induced changes in metabolite profiles in lettuce could partly explain the differential susceptibility of various lettuce types to Salmonella, although the primary or secondary metabolites mediating this effect remain unknown. Regulated mild water stress should be investigated as an approach to lower Salmonella contamination risk in suitable lettuce cultivars, while simultaneously boosting the health beneficial quality of lettuce.

Effects of Leaf Morphological and Chemical Properties on the Population Sizes of Epiphytes

To explore the main factors affecting the distribution of microbes on leaf surfaces, the relationship between population sizes of epiphytes and the morphological structure and main physical and chemical properties of leaves from stylo (Stylosanthes guianensis), alfalfa (Medicago sativa), maize (Zea mays), and cocksfoot (Dactylis glomerata) were investigated. The research results showed that the contents of soluble sugar and total phenolics on the leaf surfaces were positively correlated with those in the leaf tissues (P < 0.001). The leaves with high wax content had better moisture retention capacity. The content of soluble sugar on the leaf surfaces was positively correlated with population sizes of lactic acid bacteria (LAB), aerobic bacteria, yeasts, and molds (P < 0.001). Likewise, a positive correlation was found between the content of inorganic phosphorus on the leaf surfaces and population sizes of LAB and aerobic bacteria. The total amount of wax on leaf surfaces was negatively related to population sizes of microbes, especially aerobic bacteria (P < 0.01) and molds (P < 0.001). On the contrary, the presence of trichomes provides a shelter for epiphytes and was positively correlated with population sizes of epiphytes at different degrees of significance. In conclusion, population sizes of epiphytes on the leaf surfaces were not only affected by chemical properties, but also by morphological traits of leaves.

Plant species-dependent transmission of Escherichia coli O157:H7 from the spermosphere to cotyledons and first leaves

The colonization of six edible plant species: alfalfa, broccoli, coriander, lettuce, parsley and rocket, by the human pathogen Shigatoxigenic Escherichia coli was investigated following two modes of artificial inoculation of seeds, by soaking or watering. The frequency and extent of colonization of cotyledons depended on the mode of inoculation, with three, rapidly germinating species being successfully colonized after overnight soaking, but slower germinating species requiring prolonged exposure to bacteria by watering of the surrounding growth media. Separate analysis of the cotyledons and leaves from individual plants highlighted that successful colonization of the true leaves was also species dependent. For three species, failure of transfer, or lack of nutrients or suitable microhabitat on the leaf surface resulted in infrequent bacterial colonization. Colonization of leaves was lower and generally in proportion to that in cotyledons, if present. The potential risks associated with consumption of leafy produce are discussed.

Effects of Variety, Plant Location, and Season on the Phyllosphere Bacterial Community Structure of Alfalfa (Medicago sativa L.)

Plant phyllosphere bacteria are vital for plant health and productivity and are affected by both abiotic and biotic factors. In this study, we surveyed the structure of the phyllosphere bacterial community associated with alfalfa. For two varieties of alfalfa, forty-eight samples of phyllosphere communities were collected at two locations over four seasons in 2020. Proteobacteria and actinobacteria were associated with the dominating phylum in the bacterial communities of the alfalfa phyllosphere. Sphingomonas was the most abundant genus-level bacteria, followed by Methylobacterium, Burkholderia-Caballeronia-Paraburkholderia, and Pseudomonas. Sampling time had a greater affect than site and variety on alfalfa surface microorganisms. The variation in phyllosphere bacterial community assembly was mostly explained by the season–site interaction (43%), season–variety interaction (35%), and season (28%). Variety, site–variety interaction, and season–site–variety interactions did not have a meaningful effect on phyllosphere bacterial diversity and community structure. The bacterial community in the phyllosphere of alfalfa showed seasonal changes over time. The environmental factors that contributed most to the phyllosphere bacterial community of alfalfa were temperature and sunshine duration, which were significantly positively correlated with most of the dominant bacterial genera in the alfalfa phyllosphere.

Microbiota manipulation through the secretion of effector proteins is fundamental to the wealth of lifestyles in the fungal kingdom

Fungi are well-known decomposers of organic matter that thrive in virtually any environment on Earth where they encounter wealths of other microbes. Some fungi evolved symbiotic lifestyles, including pathogens and mutualists, that have mostly been studied in binary interactions with their hosts. However, we now appreciate that such interactions are greatly influenced by the ecological context in which they take place. While establishing their symbioses, fungi not only interact with their hosts but also with the host-associated microbiota. Thus, they target the host and its associated microbiota as a single holobiont. Recent studies have shown that fungal pathogens manipulate the host microbiota by means of secreted effector proteins with selective antimicrobial activity to stimulate disease development. In this review, we discuss the ecological contexts in which such effector-mediated microbiota manipulation is relevant for the fungal lifestyle and argue that this is not only relevant for pathogens of plants and animals but also beneficial in virtually any niche where fungi occur. Moreover, we reason that effector-mediated microbiota manipulation likely evolved already in fungal ancestors that encountered microbial competition long before symbiosis with land plants and mammalian animals evolved. Thus, we claim that effector-mediated microbiota manipulation is fundamental to fungal biology.

Phyllosphere bacterial and fungal communities vary with host species identity, plant traits and seasonality in a subtropical forest

BACKGROUND

Phyllosphere microbes play important roles in host plant performance and fitness. Recent studies have suggested that tropical and temperate forests harbor diverse phyllosphere bacterial and fungal communities and their assembly is driven by host species identity and plant traits. However, no study has yet examined how seasonality (e.g. dry vs. wet seasons) influences phyllosphere microbial community assembly in natural forests. In addition, in subtropical forests characterized as the transitional zonal vegetation type from tropical to temperate forests, how tree phyllosphere microbial communities are assembled remains unknown. In this study, we quantified bacterial and fungal community structure and diversity on the leaves of 45 tree species with varying phylogenetic identities and importance values within a 20-ha lower subtropical evergreen broad-leaved forest plot in dry and wet seasons. We explored if and how the microbial community assembly varies with host species identity, plant traits and seasonality.

RESULTS

Phyllosphere microbial communities in the subtropical forest are more abundant and diverse than those in tropical and temperate forests, and the tree species share a "core microbiome" in either bacteria or fungi. Variations in phyllosphere bacterial and fungal community assembly are explained more by host species identity than by seasonality. There is a strong clustering of the phyllosphere microbial assemblage amongst trees by seasonality, and the seasonality effects are more pronounced on bacterial than fungal community assembly. Host traits have different effects on community compositions and diversities of both bacteria and fungi, and among them calcium concentration and importance value are the most powerful explaining variables for bacteria and fungi, respectively. There are significant evolutionary associations between host species and phyllosphere microbiome.

CONCLUSIONS

Our results suggest that subtropical tree phyllosphere microbial communities vary with host species identity, plant traits and seasonality. Host species identity, compared to seasonality, has greater effects on phyllosphere microbial community assembly, and such effects differ between bacterial and fungal communities. These findings advance our understanding of the patterns and drivers of phyllosphere microbial community assembly in zonal forests at a global scale.

The effect of Epichloë endophyte on phyllosphere microbes and leaf metabolites in Achnatherum inebrians

Upon exposure to the prevailing environment, leaves become increasingly colonized by fungi and bacteria located on the surface (epiphytic) or within (endophytic) the leaves. Many cool season grasses, including Achnatherum inebrians, host a seed-borne, intercellular, mutualistic Epichloë fungal endophyte, the growth of which is synchronized with the host grass. A study utilizing illumina sequencing was used to examine the epiphytic and endophytic microbial communities in Epichloë endophyte-infected and endophyte-free A. inebrians plants growing under hot dry field conditions. The presence of Epichloë endophyte increased the Shannon and decreased Simpson diversity of bacterial and fungal communities. Sphingomonas and Hymenobacter bacteria and Filobasidium and Mycosphaerella fungi were growing largely epiphytically, whereas Methylobacterium, Escherichia-Shigella, and the fungus Blumeria were mostly found within leaves with the location of colonization influenced by the Epichloë endophyte. In addition, leaf metabolites in Epichloë-infected and Epichloë-free leaves were examined using LC/MS. Epichloë was significantly correlated with 132 metabolites.

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Epichloë altered the composition and diversity of phyllosphere microbial communities

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414 detected metabolites were annotated, of which the 132 differential metabolites

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There were 229 significant correlations between metabolites and microbial phyla

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.

New insights into the role of constitutive bacterial rhizobiome and phenolic compounds in two Pinus spp. with contrasting susceptibility to pine pitch canker

The rhizobiome is being increasingly acknowledged as a key player in plant health and breeding strategies. The pine pitch canker (PPC), caused by the fungus Fusarium circinatum, affects pine species with varying susceptibility degrees. Our aims were to explore the bacterial rhizobiome of a susceptible (Pinus radiata) and a resistant (Pinus pinea) species together with other physiological traits, and to analyze shifts upon F. circinatum inoculation. Pinus seedlings were stem inoculated with F. circinatum spores and needle gas exchange and antioxidant-related parameters were analyzed in non-inoculated and inoculated plants. Rhizobiome structure was evaluated through 16S rRNA gene massive parallel sequencing. Species (non-inoculated plants) harbored distinct rhizobiomes (<40% similarity), where P. pinea displayed a rhizobiome with increased abundance of taxa described in suppressive soils, displaying plant growth promoting (PGP) traits and/or anti-fungal activity. Plants of this species also displayed higher levels of phenolic compounds. F. circinatum induced slight changes in the rhizobiome of both species and a negative impact in photosynthetic-related parameters in P. radiata. We concluded that the rhizobiome of each pine species is distinct and higher abundance of bacterial taxa associated to disease protection was registered for the PPC-resistant species. Furthermore, differences in the rhizobiome are paralleled by a distinct content in phenolic compounds, which are also linked to plants' resistance against PPC. This study unveils a species-specific rhizobiome and provides insights to exploit the rhizobiome for plant selection in nurseries and for rhizobiome-based plant-growth-promoting strategies, boosting environmentally friendly disease control strategies.

Plant Bioactive Compounds as an Intrinsic and Sustainable Tool to Enhance the Microbial Safety of Crops

Outbreaks of produce-associated foodborne illness continue to pose a threat to human health worldwide. New approaches are necessary to improve produce safety. Plant innate immunity has potential as a host-based strategy for the deactivation of enteric pathogens. In response to various biotic and abiotic threats, plants mount defense responses that are governed by signaling pathways. Once activated, these result in the release of reactive oxygen and nitrogen species in addition to secondary metabolites that aim at tempering microbial infection and pest attack. These phytochemicals have been investigated as alternatives to chemical sanitization, as many are effective antimicrobial compounds in vitro. Their antagonistic activity toward enteric pathogens may also provide an intrinsic hurdle to their viability and multiplication in planta. Plants can detect and mount basal defenses against enteric pathogens. Evidence supports the role of plant bioactive compounds in the physiology of Salmonella enterica, Escherichia coli, and Listeria monocytogenes as well as their fitness on plants. Here, we review the current state of knowledge of the effect of phytochemicals on enteric pathogens and their colonization of plants. Further understanding of the interplay between foodborne pathogens and the chemical environment on/in host plants may have lasting impacts on crop management for enhanced microbial safety through translational applications in plant breeding, editing technologies, and defense priming.

Comparative fungal diversity and dynamics in plant compartments at different developmental stages under root-zone restricted grapevines

BACKGROUND

The root-zone restriction cultivation technique is used to achieve superior fruit quality at the cost of limited vegetative and enhanced reproductive development of grapevines. Fungal interactions and diversity in grapevines are well established; however, our knowledge about fungal diversity under the root-zone restriction technique is still unexplored. To provide insights into the role of mycobiota in the regulation of growth and fruit quality of grapevine under root-zone restriction, DNA from rhizosphere and plant compartments, including white roots (new roots), leaves, flowers, and berries of root-zone restricted (treatment) and conventionally grown plants (control), was extracted at three growth stages (full bloom, veraison, and maturity).

RESULTS

Diversity analysis based on the ITS1 region was performed using QIIME2. We observed that the root-zone restriction technique primarily affected the fungal communities of the soil and plant compartments at different growth stages. Interestingly, Fusarium, Ilyonectria, Cladosporium and Aspergillus spp observed in the rhizosphere overlapped with the phyllosphere at all phenological stages, having distinctive abundance in grapevine habitats. Peak richness and diversity were observed in the rhizosphere at the full bloom stage of control plants, white roots at the veraison stage of treatment, leaves at the maturity stage of treatment, flowers at the full bloom stage and berries at the veraison stage of control plants. Except for white roots, the diversity of soil and plant compartments of treated plants tended to increase until maturity. At the maturity stage of the treated and control plants, the abundance of Aspergillus spp. was 25.99 and 29.48%, respectively. Moreover, the total soluble sugar content of berries was 19.03 obrix and 16 obrix in treated and control plants, respectively, at the maturity stage.

CONCLUSIONS

This is the first elucidative study targeting the fungal diversity of conventional and root-restricted cultivation techniques in a single vineyard. Species richness and diversity are affected by stressful cultivation known as root zone restriction. There is an association between the abundance of Aspergillus spp. and fruit quality because despite causing stress to the grapevine, superior quality of fruit is retrieved in root-zone restricted plants.

Persistence of Escherichia coli in the microbiomes of red Romaine lettuce (Lactuca sativa cv. 'Outredgeous') and mizuna mustard (Brassica rapa var. japonica) - does seed sanitization matter?

BACKGROUND

Seed sanitization via chemical processes removes/reduces microbes from the external surfaces of the seed and thereby could have an impact on the plants' health or productivity. To determine the impact of seed sanitization on the plants' microbiome and pathogen persistence, sanitized and unsanitized seeds from two leafy green crops, red Romaine lettuce (Lactuca sativa cv. 'Outredgeous') and mizuna mustard (Brassica rapa var. japonica) were exposed to Escherichia coli and grown in controlled environment growth chambers simulating environmental conditions aboard the International Space Station. Plants were harvested at four intervals from 7 days post-germination to maturity. The bacterial communities of leaf and root were investigated using the 16S rRNA sequencing while quantitative polymerase chain reaction (qPCR) and heterotrophic plate counts were used to reveal the persistence of E. coli.

RESULT

E. coli was detectable for longer periods of time in plants from sanitized versus unsanitized seeds and was identified in root tissue more frequently than in leaf tissue. 16S rRNA sequencing showed dynamic changes in the abundance of members of the phylum Proteobacteria, Firmicutes, and Bacteroidetes in leaf and root samples of both leafy crops. We observed minimal changes in the microbial diversity of lettuce or mizuna leaf tissue with time or between sanitized and unsanitized seeds. Beta-diversity showed that time had more of an influence on all samples versus the E. coli treatment.

CONCLUSION

Our results indicated that the seed surface sanitization, a current requirement for sending seeds to space, could influence the microbiome. Insight into the changes in the crop microbiomes could lead to healthier plants and safer food supplementation.

Leaf surface microtopography shaping the bacterial community in the phyllosphere: evidence from 11 tree species

Phyllosphere bacteria are an important component of environmental microbial communities and are closely related to plant health and ecosystem stability. However, the relationships between the inhabitation and assembly of phyllosphere bacteria and leaf microtopography are still obscure. In this study, the phyllosphere bacterial communities and leaf microtopographic features (vein density, stomatal length, and density) of eleven tree species were fully examined. Both the absolute abundance and diversity of phyllosphere bacterial communities were significantly different among the tree species, and leaf vein density dominated the variation. TITAN analysis showed that leaf vein density also played more important roles in regulating the relative abundance of bacteria than stomatal features, and 6 phyla and 62 genera of phyllosphere bacteria showed significant positive responses to leaf vein density. Moreover, LEfSe analysis showed that the leaves with higher vein density had more bacterial biomarkers. Leaf vein density also changed the co-occurrence pattern of phyllosphere bacteria, and the co-occurrence network demonstrated more negative correlations and more nodes on the leaves with larger leaf vein density, indicating that higher densities of leaf veins improved the stability of the phyllosphere bacterial community. Phylogenetic analysis showed that deterministic processes (especially homogeneous selection) dominated the assembly process of phyllosphere bacterial communities. The leaf vein density increased the degree of bacterial clustering at the phylogenetic level. Therefore, the inhabitation and assembly of the phyllosphere bacterial community are related to leaf microtopography, which provides deeper insight into the interaction between plants and bacteria.

Spatial Characterization of Microbial Communities on Multi-Species Leafy Greens Grown Simultaneously in the Vegetable Production Systems on the International Space Station

The establishment of steady-state continuous crop production during long-term deep space missions is critical for providing consistent nutritional and psychological benefits for the crew, potentially improving their health and performance. Three technology demonstrations were completed achieving simultaneous multi-species plant growth and the concurrent use of two Veggie units on the International Space Station (ISS). Microbiological characterization using molecular and culture-based methods was performed on leaves and roots from two harvests of three leafy greens, red romaine lettuce (Lactuca sativa cv. ‘Outredgeous’); mizuna mustard, (Brassica rapa var japonica); and green leaf lettuce, (Lactuca sativa cv. Waldmann’s) and associated rooting pillow components and Veggie chamber surfaces. Culture based enumeration and pathogen screening indicated the leafy greens were safe for consumption. Surface samples of the Veggie facility and plant pillows revealed low counts of bacteria and fungi and are commonly isolated on ISS. Community analysis was completed with 16S rRNA amplicon sequencing. Comparisons between pillow components, and plant tissue types from VEG-03D, E, and F revealed higher diversity in roots and rooting substrate than the leaves and wick. This work provides valuable information for food production-related research on the ISS and the impact of the plant microbiome on this unique closed environment.

The Macleaya cordata Symbiont: Revealing the Effects of Plant Niches and Alkaloids on the Bacterial Community

Endophytes are highly associated with plant growth and health. Exploring the variation of bacterial communities in different plant niches is essential for understanding microbe-plant interactions. In this study, high-throughput gene sequencing was used to analyze the composition and abundance of bacteria from the rhizospheric soil and different parts of the Macleaya cordata. The results indicated that the bacterial community structure varied widely among compartments. Bacterial diversity was observed to be the highest in the rhizospheric soil and the lowest in fruits. Proteobacteria, Actinobacteria, and Bacteroidetes were found as the dominant phyla. The genera Sphingomonas (∼47.77%) and Methylobacterium (∼45.25%) dominated in fruits and leaves, respectively. High-performance liquid chromatography (HPLC) was employed to measure the alkaloid content of different plant parts. Significant correlations were observed between endophytic bacteria and alkaloids. Especially, Sphingomonas showed a significant positive correlation with sanguinarine and chelerythrine. All four alkaloids were negatively correlated with the microbiota of stems. The predicted result of PICRUST2 revealed that the synthesis of plant alkaloids might lead to a higher abundance of endophytic microorganisms with genes related to alkaloid synthesis, further demonstrated the correlation between bacterial communities and alkaloids. This study provided the first insight into the bacterial community composition in different parts of Macleaya cordata and the correlation between the endophytic bacteria and alkaloids.

Colonization of toxic cyanobacteria on the surface and inside of leafy green: A hidden source of cyanotoxin production and exposure

Cyanobacteria are a threat to the safety of water sources for drinking, recreation, and food production, because some cyanobacteria, such as Microcystis, produce cyanotoxins. However, the colonization of plants by Microcystis and the fate of their toxin, microcystins (MCs), in agricultural environments have not been thoroughly studied. This study examined the colonization of lettuce, as a representative of leafy greens, by Microcystis and its potential impact on food safety and crop health. The surfaces of lettuce leaves were exposed to environmentally relevant concentrations of M. aeruginosa (104, 106, and 108mcyE gene copies/mL) by mimicking contamination scenarios during cultivation, such as spraying irrigation with contaminated water or deposits of airborne Microcystis. Scanning electron microscope (SEM) and droplet digital PCR were used. The results showed that M. aeruginosa colonized the surface of leaves and MCs accumulated in the edible part of the lettuce (>20 μg/kg of lettuce). Crop productivity (length, weight, and number of leaves) was negatively affected. The SEM images provide evidence that M. aeruginosa deposited on the lettuce surface can be internalized via natural opening sites of the leaves and then proliferate within the plants. Our findings imply that toxic cyanobacteria contamination in agricultural environments can be a significant cyanotoxin exposure pathway.

Divergence of Phyllosphere Microbial Communities Between Females and Males of the Dioecious Populus cathayana

Females and males of dioecious plants have evolved sex-specific characteristics in terms of their morphological and physiological properties. However, the differentiation of phyllosphere microbiota in dioecious plants remains largely unexplored. Here, the diversity and composition of female and male Populus cathayana phyllosphere bacterial and fungal communities were investigated using 16S rRNA/ITS1 gene-based MiSeq sequencing. The divergences of bacterial and fungal community compositions occurred between females and males. Both females and males had their unique phyllosphere bacterial and fungal microbiota, such as bacterial Gemmata spp. (5.41%) and fungal Pringsheimia spp. (0.03%) in females and bacterial Chitinophaga spp. (0.009%) and fungal Phaeococcomyces spp. (0.02%) in males. Significant differences in the relative abundance of phyla Proteobacteria and Planctomycetes bacteria and phyla Ascomycota and Basidiomycota fungi (P < 0.05) were also found between females and males. Some bacterial species of genera Spirosoma and Amnibacterium and fungal genera Venturia, Suillus, and Elmerina spp. were significantly enriched in males (P < 0.05). In contrast, levels of fungal genera Phoma and Aureobasidium spp. were significantly higher in females than in males (P < 0.05). The mineral, inorganic, and organic nutrients content contributed differently to the divergence of female and male phyllosphere microbial communities, with 87.08 and 45.17% of the variations being explained for bacterial and fungal communities, respectively. These results highlight the sexual discrimination of phyllosphere microbes on the dioecious plants and provide hints on the potential host-associated species in phyllosphere environments.[Formula: see text] Copyright © 2021 The Author(s). This is an open access article distributed under the CC BY 4.0 International license.

Caterpillar gut and host plant phylloplane mycobiomes differ: a new perspective on fungal involvement in insect guts

Compared with the highly diverse microbiota of leaves, herbivorous insects exhibit impoverished gut microbial communities. Research to date has focused on the bacterial component of these gut microbiomes, neglecting the fungal component. As caterpillar gut bacterial microbiomes are derived strongly from their diet, we hypothesized that their mycobiomes would reflect the host leaf mycobiomes. Using the ITS2 rDNA and V5-V6 16S rRNA gene regions for DNA metabarcoding of caterpillar gut and host leaf sample pairs we compared their mycobiome genus diversity and compositions and identified genera associated with caterpillar guts. Leaves and caterpillar guts harbored different mycobiomes with quite low qualitative similarity (Jaccard index = 38.03%). The fungal genera most significantly associated with the caterpillar gut included Penicillium, Mucor and unidentified Saccharomycetales, whereas leaf-associated genera included Holtermanniella, Gibberella (teleomorph of Fusarium) and Seimatosporium. Although caterpillar gut and leaf mycobiomes had similar genus richness overall, this indicator was not correlated for individual duplets. Moreover, as more samples entered the analysis, mycobiome richness increased more rapidly in caterpillar guts than in leaves. The results suggest that the mycobiota of the caterpillar gut differs from that of their feeding substrate; further, the mycobiomes appear to be richer than the well-studied bacterial microbiotas.

Ozone uptake at night is more damaging to plants than equivalent day-time flux

MAIN CONCLUSION

Plants exposed to equivalent ozone fluxes administered during day-time versus night-time exhibited greater losses in biomass at night and this finding is attributed to night-time depletion of cell wall-localised ascorbate. The present study employed Lactuca sativa and its closest wild relative, L. serriola, to explore the relative sensitivity of plants to ozone-induced oxidative stress during day-time versus night-time. By controlling atmospheric ozone concentration and measuring stomatal conductance, equivalent ozone uptake into leaves was engineered during day and night, and consequences on productivity and net CO2 assimilation rate were determined. Biomass losses attributable to ozone were significantly greater when an equivalent dose of ozone was taken-up by foliage at night compared to the day. Linkages between ozone impacts and ascorbic acid (AA) content, redox status and cellular compartmentation were probed in both species. Leaf AA pools were depleted by exposure of plants to darkness, and then AA levels in the apoplast and symplast were monitored on subsequent transfer of plants to the light. Apoplast AA appeared to be more affected by light-dark transition than the symplast pool. Moreover, equivalent ozone fluxes administered to leaves with contrasting AA levels resulted in contrasting effects on the light-saturated rate of CO2 assimilation (Asat) in both species. Once apoplast AA content recovered to pre-treatment levels, the same ozone flux resulted in no impacts on Asat. The results of the present investigation reveal that plants are significantly more sensitive to equivalent ozone fluxes taken-up at night compared with those during the day and were consistent with diel shifts in apoplast AA content and/or redox status. Furthermore, findings suggest that some thought should be given to weighing regional models of ozone impacts for extraordinary night-time ozone impacts.

Exploration of Intrinsic Microbial Community Modulators in the Rice Endosphere Indicates a Key Role of Distinct Bacterial Taxa Across Different Cultivars

Microbial communities associated with the plant phyllosphere and endosphere can have both beneficial as well as detrimental effects on their hosts. There is an ongoing debate to which extend the phyllosphere and endosphere microbiome assembly is controlled by the host plant how pronounced cultivar effects are. We investigated the bacterial and fungal communities from the phyllosphere and endosphere of 10 different rice cultivars grown under identical environmental conditions in the frame of a targeted approach to identify drivers of community assembly. The results indicated that the endophytic bacterial communities were clearly separated into two groups. The α-diversity and microbial network complexity within Group I were significantly lower than in Group II. Moreover, the genera Nocardioides, Microvirga, and Gaiella were significantly more abundant in Group II and only present in the interaction networks of this group. These three genera were significantly correlated with α- and β-diversity of the endophytic bacterial community and thus identified as major drivers of the endosphere community. We have identified keystone taxa that shape endophytic bacterial communities of different rice cultivars. Our overall findings provide new insights into plant-microbe interactions, and may contribute to targeted improvements of rice varieties in the future.

Terroir Is the Main Driver of the Epiphytic Bacterial and Fungal Communities of Mango Carposphere in Reunion Island

The diversity of both bacterial and fungal communities associated with mango surface was explored using a metabarcoding approach targeting fungal ITS2 and bacterial 16S (V3-V4) genomic regions. Fruits were collected in Reunion Island from two different orchards according to a sampling method which allowed the effect of several pre-harvest factors such as geographical location (terroir), cultivars, fruit parts, tree position in the plot, fruit position on the tree (orientation and height), as well as the harvest date to be investigated. A total of 4,266,546 fungal and 2,049,919 bacterial reads were recovered then respectively assigned to 3,153 fungal and 24,087 to bacterial amplicon sequence variants (ASVs). Alpha and beta diversity, as well as differential abundance analyses revealed variations in both bacterial and fungal communities detected on mango surfaces depended upon the studied factor. Results indicated that Burkholderiaceae (58.8%), Enterobacteriaceae (5.2%), Pseudomonadaceae (4.8%), Sphingomonadaceae (4.1%), Beijerinckiaceae (3.5%), and Microbacteriaceae (3.1%) were the dominant bacterial families across all samples. The majority of fungal sequences were assigned to Mycosphaerellaceae (34.5%), Cladosporiaceae (23.21%), Aureobasidiaceae (13.09%), Pleosporaceae (6.92%), Trichosphaeriaceae (5.17%), and Microstromatales_fam_Incertae_sedis (4.67%). For each studied location, mango fruit from each cultivar shared a core microbiome, and fruits of the same cultivar harvested in two different locations shared about 80% fungal and bacterial family taxa. The various factors tested in this study affected bacterial and fungal taxa differently, suggesting that some taxa could act as geographical (terroir) markers and in some cases as cultivar fingerprints. The ranking of the factors investigated in the present study showed that in decreasing order of importance: the plot (terroir), cultivar, fruit parts, harvest date and the position of the fruits are respectively the most impacting factors of the microbial flora, when compared to the orientation and the fruit position (height) on the tree. Overall, these findings provided insights on both bacterial and fungal diversity associated with the mango surface, their patterns from intra-fruit scale to local scale and the potential parameters shaping the mango microbiota.

Microbial Flow Within an Air-Phyllosphere-Soil Continuum

The phyllosphere is populated by numerous microorganisms. Microbes from the wider environment, i.e., air and soil, are considered key contributors to phyllosphere microbial communities, but their contribution is unclear. This study seeks to address this knowledge gap by controlling the movement of microbes along the air-phyllosphere-soil continuum. Customized equipment with dual chambers was constructed that permitted airflow to enter the first chamber while the second chamber recruited filtered microbe-free air from the initial chamber. Allium schoenoprasum (chive) and Sonchus oleraceus (sow thistle) were cultivated in both chambers, and the microbial communities from air, phyllosphere, and soil samples were characterized. Shares of microbial OTUs in the equipment suggested a potential interconnection between the air, phyllosphere, and soil system. Fast expectation-maximization microbial source tracking (FEAST) suggested that soil was the major source of airborne microbial communities. In contrast, the contribution of airborne and soil microbes to phyllosphere microbial communities of either A. schoenoprasum or S. oleraceus was limited. Notably, the soilborne microbes were the only environmental sources to phyllosphere in the second chamber and could affect the composition of phyllosphere microbiota indirectly by air flow. The current study demonstrated the possible sources of phyllosphere microbes by controlling external airborne microbes in a designed microcosm system and provided a potential strategy for recruitment for phyllosphere recruitment.

Induction of antibiotic specialized metabolism by co-culturing in a collection of phyllosphere bacteria

A diverse set of bacteria live on the above-ground parts of plants, composing the phyllosphere, and play important roles for plant health. Phyllosphere microbial communities assemble in a predictable manner and diverge from communities colonizing other plant organs or the soil. However, how these communities differ functionally remains obscure. We assembled a collection of 258 bacterial isolates representative of the most abundant taxa of the phyllosphere of Arabidopsis and a shared soil inoculum. We screened the collection for the production of metabolites that inhibit the growth of Gram-positive and Gram-negative bacteria either in isolation or in co-culture. We found that isolates capable of constitutive antibiotic production in monoculture were significantly enriched in the soil fraction. In contrast, the proportion of binary cultures resulting in the production of growth inhibitory compounds differed only marginally between the phyllosphere and soil fractions. This shows that the phyllosphere may be a rich resource for potentially novel molecules with antibiotic activity, but that production or activity is dependent upon induction by external signals or cues. Finally, we describe the isolation of antimicrobial acyloin metabolites from a binary culture of Arabidopsis phyllosphere isolates, which inhibit the growth of clinically relevant Acinetobacter baumannii.

Bacterial communities in the plant phyllosphere harbour distinct responders to a broad-spectrum pesticide

Pesticide application can be accompanied by harmful non-target effects that affect humans, animals, as well as whole ecosystems. However, such effects remain mainly unaddressed in connection with microorganisms, and especially bacteria therein, which are essential for ecosystem functioning and host health. We analysed bacterial communities by sequencing 16S rRNA gene fragment amplicons following spray application of a broad-spectrum fungicide based on the active ingredient N-(3,5-dichlorophenyl) succinimide on Nicotiana tabacum L. leaves. The plant's phyllosphere was predominantly colonized by Proteobacteria, with Alphaproteobacteria accounting for up to 33.8% of the indigenous bacterial community. Bioinformatic analyses indicated that pesticide applications had an effect on the core microbiome as well as the rare microbiome. Moreover, the interference of the pesticide with phyllosphere bacteria was found to be selective. We have identified four positive responders including an ASV assigned to the genus Acinetobacter and 12 negative responders mainly assigned to bacterial genera known for beneficial plant-microbe interactions, including Stenotrophomonas, Sphingomonas, Flavobacterium and Serratia. Complementary inference of bacterial functioning on community level indicated that microbes with distinct stress response systems were likely enriched in the conducted treatments. The overall findings confirmed that pesticide treatments can induce measureable shifts in non-target bacterial communities colonizing the plant phyllosphere. They also indicate that potentially beneficial bacteria, which are known for their intrinsic association with plants, are among the most sensitive responders to the employed fungicide and thus highlight the importance of off-target studies in the context of the plant microbiome.

Effects of Plant and Soil Characteristics on Phyllosphere and Rhizosphere Fungal Communities During Plant Development in a Copper Tailings Dam

Interactions between plants and microbes can affect ecosystem functions, and many studies have demonstrated that plant properties influence mutualistic microorganisms. Here, high-throughput sequencing was used to investigate rhizosphere and phyllosphere fungal communities during different plant development stages. Results demonstrated that phyllosphere and rhizosphere fungal community structures were distinct during all developmental stages while they were mediated separately by plant carbon and soil sulfur. Comparatively, the effect of root properties on phyllosphere fungal diversity was greater than soil properties. Moreover, rhizosphere fungal networks of Bothriochloa ischaemum were more complex than phyllosphere fungal networks. This study demonstrated that the effect of plant and soil traits on phyllosphere and rhizosphere fungal communities could potentially be significant, depending on the applicable environmental condition and plant development stage. Although links between phyllosphere and rhizosphere communities have been established, further studies on functional fungal groups during phytoremediation processes are necessary. This study comprehensively analyzed dynamic relationships between phyllosphere and rhizosphere fungal communities during different plant development stages in a polluted environment. These fungal communities were determined to be expedient to the development and utilization of beneficial microbial communities during different development stages, which could more effectively help to stabilize and reclaim contaminated copper tailings soil.

Microbial colonization on the leaf surfaces of different genotypes of Napier grass

To address correlations between population sizes of microbes on the leaf surfaces and leaf morphological and physicochemical properties, various leaf morphological and physicochemical features as possible predictors of microbial population sizes on the leaf surfaces of four Napier grass cultivars were assessed. Results indicated microbes except for lactic acid bacteria (LAB) preferred to colonize the leaf surfaces bearing trichomes, and their population sizes were significantly correlated with trichomes, especially for yeasts. The population sizes of microbes were positively correlated with soluble sugar content (p < 0.05). Furthermore, no significant correlation was found between population sizes of microbes and wax content, except for yeasts. The multivariate regression trees (MRT) analysis showed different genotypes of leaf-microbe system could be characterized by four-leaf attributes with soluble sugar of leaf tissues being the primary explanatory attribute. Leaves with soluble sugar content below 9.72 mg g^-1 fresh weight (FW) were rarely colonized. For leaves with soluble sugar content above 9.72 mg g^-1 FW, water content was the next explanatory leaf attribute, followed by wax content on the leaf surfaces. Leaves with higher water content (> 73%) were more colonized, and small microbial population was associated with higher wax content (> 10.66 mg g^-1 dry matter). In conclusion, leaf chemical attributes have a higher contribution than morphological structure properties in determining population sizes of microbes on the leaf surfaces. The exuded soluble sugar and protein promote the development of microbial populations. For different genotypes of leaf-microbe system, the relationship between microbial abundance on their leaf surfaces and leaf morphological structure or physicochemical properties may be predicted by the MRT. Population sizes of microbes are primarily influenced by soluble sugar content under the water-rich conditions.

The unexplored bacterial lifestyle on leaf surface

Social interactions impact microbial communities and these relationships are mediated by small molecules. The chemical ecology of bacteria on the phylloplane environment is still little explored. The harsh environmental conditions found on leaf surface require high metabolic performances of the bacteria in order to survive. That is interesting both for scientific fields of prospecting natural molecules and for the ecological studies. Important queries about the bacterial lifestyle on leaf surface remain not fully comprehended. Does the hostility of the environment increase the populations' cellular altruism by the production of molecules, which can benefit the whole community? Or does the reverse occur and the production of molecules related to competition between species is increased? Does the phylogenetic distance between the bacterial populations influence the chemical profile during social interactions? Do phylogenetically related bacteria tend to cooperate more than the distant ones? The phylloplane contains high levels of yet uncultivated microorganisms, and understanding the molecular basis of the social networks on this habitat is crucial to gain new insights on the ecology of the mysterious community members due to interspecies molecular dependence. Here, we review and discuss what is known about bacterial social interactions and their chemical lifestyle on leaf surface.

Epiphytic and Endophytic Bacteria on Olive Tree Phyllosphere: Exploring Tissue and Cultivar Effect

Variation on bacterial communities living in the phyllosphere as epiphytes and endophytes has been attributed to plant host effects. However, there is contradictory or inconclusive evidence regarding the effect of plant genetics (below the species' level) and of plant tissue type on phyllosphere bacterial community assembly, in particular when epiphytes and endophytes are considered simultaneously. Here, both surface and internal bacterial communities of two olive (Olea europaea) cultivars were evaluated in twigs and leaves by molecular identification of cultivable isolates, with an attempt to answer these questions. Overall, Proteobacteria, Actinobacteria and Firmicutes were the dominant phyla, being epiphytes more diverse and abundant than endophytes. Host genotype (at cultivar level) had a structuring effect on the composition of bacterial communities and, in a similar way, for both epiphytes and endophytes. Plant organ (leaf vs. twig) control of the bacterial communities was less evident when compared with plant genotype and with a greater influence on epiphytic than on endophytic community structure. Each olive genotype/plant organ was apparently selective towards specific bacterial operational taxonomic units (OTUs), which may lead to specific feedbacks on fitness of plant genotypes. Bacterial recruitment was observed to happen mainly within epiphytes than in endophytes and in leaves as compared with twigs. Such host specificity suggested that the benefits derived from the plant-bacteria interaction should be considered at genetic levels below the species.

Revealing structure and assembly for rhizophyte-endophyte diazotrophic community in mangrove ecosystem after introduced Sonneratia apetala and Laguncularia racemosa

Biological nitrogen fixation (BNF) mediated by diazotrophic communities is a major source of bioavailable nitrogen in mangrove wetlands, which plays important roles in maintaining the health and stability of mangrove ecosystems. Recent large-scale mangrove afforestation activities have drawn great attention due to introduced mangrove species and their potential impacts on bio-functionalities of local ecosystems. However, the effects of introduced mangrove species on diazotrophic communities remain unclear. Here, we analyzed rhizosphere and endosphere diazotrophic communities between native mangrove species (Avicennia marina) and introduced mangrove species (Sonneratia apetala and Laguncularia racemose) by sequencing nifH gene amplicons. Our results showed that S. apetala and L. racemose introduction significantly (P < 0.05) increased nutrition components (e.g., total carbon and total nitrogen) in rhizosphere, as well as the diazotrophs richness in rhizosphere and endosphere. The relative abundance of clusters III diazotrophs in the rhizosphere and Rhizobium in the endosphere were significantly increased with L. racemosa or S. apetala introduction. Fe and pH were the main environmental factors driving the divergence of endophyte-rhizophyte diazotrophs between native and introduced mangroves. The correlation-based network analyses indicated that the interaction among rhizophyte-endophyte diazotrophs is more harmonious in native mangrove, while there exist more competition in introduced mangroves. These findings expand our current understanding of BNF in mangrove afforestation, and providing new perspectives to sustainable management of mangrove ecosystem.

Dynamics Relationship of Phyllosphere and Rhizosphere Bacterial Communities During the Development of Bothriochloa ischaemum in Copper Tailings

Copper mining and the byproducts associated with the industry have led to serious pollution in the Loess Plateau of China. There is a potential in improving the ecological restoration efficiency of such degraded land through combining microbial and plant remediation approaches. However, the community structure and function of phyllosphere and rhizosphere microorganisms and their response to plant development in copper tailings dams are poorly understood. This study investigated the impact of the phyllosphere and rhizosphere microbial communities on Bothriochloa ischaemum during three distinct plant development stages: seedling, tiller, and mature. The relative species abundance and Shannon index of bacterial communities of the rhizosphere during the seedling and tiller stages were distinct from that in the mature stage. Dominant bacteria at the level of phyla, such as Proteobacteria, Cyanobacteria, Actinobacteria, and Bacteroidetes, followed distinct patterns associated with plant development in the phyllosphere, but the predominant bacteria were similar in the rhizosphere. Redundancy analysis showed that aboveground total nitrogen and the carbon and nitrogen ratio of this plant species significantly affected phyllosphere bacterial community structure, whereas soil water content, soil nutrients, electrical conductivity, and salinity significantly affected rhizosphere bacterial community structure. Moreover, keystone phyllosphere and rhizosphere bacterial species differed significantly. This study sheds new light on understanding the dynamic relationship of phyllosphere and rhizosphere bacterial communities during plant development in copper tailings. These results are beneficial to the development and utilization of beneficial microbial communities at different stages of development, which might help to reclaim and stabilize tailings more effectively.

Adaptive matching between phyllosphere bacteria and their tree hosts in a neotropical forest

BACKGROUND

The phyllosphere is an important microbial habitat, but our understanding of how plant hosts drive the composition of their associated leaf microbial communities and whether taxonomic associations between plants and phyllosphere microbes represent adaptive matching remains limited. In this study, we quantify bacterial functional diversity in the phyllosphere of 17 tree species in a diverse neotropical forest using metagenomic shotgun sequencing. We ask how hosts drive the functional composition of phyllosphere communities and their turnover across tree species, using host functional traits and phylogeny.

RESULTS

Neotropical tree phyllosphere communities are dominated by functions related to the metabolism of carbohydrates, amino acids, and energy acquisition, along with environmental signalling pathways involved in membrane transport. While most functional variation was observed within communities, there is non-random assembly of microbial functions across host species possessing different leaf traits. Metabolic functions related to biosynthesis and degradation of secondary compounds, along with signal transduction and cell-cell adhesion, were particularly important in driving the match between microbial functions and host traits. These microbial functions were also evolutionarily conserved across the host phylogeny.

CONCLUSIONS

Functional profiling based on metagenomic shotgun sequencing offers evidence for the presence of a core functional microbiota across phyllosphere communities of neotropical trees. While functional turnover across phyllosphere communities is relatively small, the association between microbial functions and leaf trait gradients among host species supports a significant role for plant hosts as selective filters on phyllosphere community assembly. This interpretation is supported by the presence of phylogenetic signal for the microbial traits driving inter-community variation across the host phylogeny. Taken together, our results suggest that there is adaptive matching between phyllosphere microbes and their plant hosts. Video abstract.

Microbial Monitoring in the EDEN ISS Greenhouse, a Mobile Test Facility in Antarctica

The EDEN ISS greenhouse, integrated in two joined containers, is a confined mobile test facility in Antarctica for the development and optimization of new plant cultivation techniques for future space programs. The EDEN ISS greenhouse was used successfully from February to November 2018 for fresh food production for the overwintering crew at the Antarctic Neumayer III station. During the 9 months of operation, samples from the different plants, from the nutrition solution of the aeroponic planting system, and from diverse surfaces within the three different compartments of the container were taken [future exploration greenhouse (FEG), service section (SS), and cold porch (CP)]. Quantity as well as diversity of microorganisms was examined by cultivation. In case of the plant samples, microbial quantities were in a range from 102 to 104 colony forming units per gram plant material. Compared to plants purchased from a German grocery, the produce hosted orders of magnitude more microorganisms than the EDEN ISS plants. The EDEN ISS plant samples contained mainly fungi and a few bacteria. No classical food associated pathogenic microorganism, like Escherichia and Salmonella, could be found. Probably due to the used cultivation approach, Archaea were not found in the samples. The bioburden in the nutrition solutions increased constantly over time but never reached critical values like 102-103 cfu per 100 mL in irrigation water as it is stated, e.g., for commercial European plant productions. The surface samples revealed high differences in the microbial burden between the greenhouse part of the container and the SS and CP part. However, the numbers of organisms (bacteria and fungi) found in the planted greenhouse were still not critical. The microbial loaded surfaces showed strong temporal as well as spatial fluctuations. In samples of the nutrition solution and the surface, the amount of bacteria exceeded the amount of fungi by many times. For identification, 16S rRNA gene sequencing was performed for the isolated prokaryotic organisms. Phylogenetic analyses revealed that the most abundant bacterial phyla were Firmicutes and Actinobacteria. These phyla include plant- and human-associated bacterial species. In general, it could be shown that it is possible to produce edible fresh food in a remote environment and this food is safe for consumption from a microbiological point of view.

Phyllospheric Microbiomes: Diversity, Ecological Significance, and Biotechnological Applications

The phyllosphere referred to the total aerial plant surfaces (above-ground portions), as habitat for microorganisms. Microorganisms establish compositionally complex communities on the leaf surface. The microbiome of phyllosphere is rich in diversity of bacteria, fungi, actinomycetes, cyanobacteria, and viruses. The diversity, dispersal, and community development on the leaf surface are based on the physiochemistry, environment, and also the immunity of the host plant. A colonization process is an important event where both the microbe and the host plant have been benefited. Microbes commonly established either epiphytic or endophytic mode of life cycle on phyllosphere environment, which helps the host plant and functional communication with the surrounding environment. To the scientific advancement, several molecular techniques like metagenomics and metaproteomics have been used to study and understand the physiology and functional relationship of microbes to the host and its environment. Based on the available information, this chapter describes the basic understanding of microbiome in leaf structure and physiology, microbial interactions, especially bacteria, fungi, and actinomycetes, and their adaptation in the phyllosphere environment. Further, the detailed information related to the importance of the microbiome in phyllosphere to the host plant and their environment has been analyzed. Besides, biopotentials of the phyllosphere microbiome have been reviewed.