Driving factors of epiphytic bacterial communities: A review

Taming of the microbial beasts: Plant immunity tethers potentially pathogenic microbiota members

Plants are in intimate association with taxonomically structured microbial communities called the plant microbiota. There is growing evidence that the plant microbiota contributes to the holistic performance and general health of plants, especially under unfavorable situations. Despite the attached benefits, surprisingly, the plant microbiota in nature also includes potentially pathogenic strains, signifying that the plant hosts have tight control over these microbes. Despite the conceivable role of plant immunity in regulating its microbiota, we lack a complete understanding of its role in governing the assembly, maintenance, and function of the plant microbiota. Here, we highlight the recent progress on the mechanistic relevance of host immunity in orchestrating plant-microbiota dialogues and discuss the pluses and perils of these microbial assemblies.

Hydration conditions as a critical factor in antibiotic-mediated bacterial competition outcomes

Antibiotic secretion plays a pivotal role in bacterial interference competition; yet, the impact of environmental hydration conditions on such competition is not well understood. Here, we investigate how hydration conditions affect interference competition among bacteria, studying the interactions between the antibiotic-producing Bacillus velezensis FZB42 and two bacterial strains susceptible to its antibiotics: Xanthomonas euvesicatoria 85-10 and Pseudomonas syringae DC3000. Our results show that wet-dry cycles significantly modify the response of the susceptible bacteria to both the supernatant and cells of the antibiotic-producing bacteria, compared to constantly wet conditions. Notably, X. euvesicatoria shows increased protection against both the cells and supernatants of B. velezensis under wet-dry cycles, while P. syringae cells become more susceptible under wet-dry cycles. In addition, we observed a reciprocal interaction between P. syringae and B. velezensis, where P. syringae inhibits B. velezensis under wet conditions. Our findings highlight the important role of hydration conditions in shaping bacterial interference competition, providing valuable insights into the microbial ecology of water-unsaturated surfaces, with implications for applications such as biological control of plant pathogens and mitigating antibiotic resistance.IMPORTANCEOur study reveals that hydration conditions, particularly wet-dry cycles, significantly influence antibiotic-mediated competition between bacterial species. We revealed that the effectiveness of antibiotics produced by Bacillus velezensis against two susceptible bacterial species: Xanthomonas and Pseudomonas varies based on these hydration conditions. Unlike traditional laboratory environments, many real-world habitats, such as soil, plant surfaces, and even animal skin, undergo frequent wet-dry cycles. These conditions affect bacterial competition dynamics and outcomes, with wet-dry cycles providing increased protection for some bacteria while making others more susceptible. Our findings highlight the importance of considering environmental hydration when studying microbial interactions and developing biological control strategies. This research has important implications for improving agricultural practices and understanding natural microbial ecosystems.

Root microbiome of Panax ginseng in comparison with three other medicinal plants in the families of Araliaceae and Apiaceae

The intricate interplay between endophytic microorganisms and plants in the upkeep of biodiversity, the stability of communities, and the operation of ecosystems needs to be more adequately extensive. Although root-associated microbial communities of plants have been revealed for the last decade, the understanding of bacterial and fungal communities associated with the roots of medicinal plants remains elusive. To highlight the importance of Panax ginseng Meyer (PG) in our research, we investigated the root endophytic bacterial and fungal communities of Panax ginseng Meyer (PG), alongside Aralia cordata (AC), Angelica gigas (AG), and Peucedanum japonicum (PJ), utilizing amplicon-based community profiling and advanced bioinformatic methodologies. The study aimed to investigate the root-endophytic microbiota of ginseng and three other medicinal plants and identify similarities in microbiome composition across different plant species and families. Results revealed that root-endophytic bacterial and fungal communities were influenced by plant species and phylogenetic differences at the family level. Differential abundance tests and random forest models showed microbial features within the same plant family. PG had a distinctive microbial profile with significant B1653_o_Enterobacterales and F8_o_Helotiales. PG had a core microbiome, B10_Allorhizobium-Neorhizobium-Pararhizobium-Rhizobium, and a more evenly distributed microbial network compared to AG, PJ, and AC. Our research reveals the intricate endophytic microbial communities within the roots of medicinal plants, pinpointing specific taxa that may be pivotal to their medicinal qualities and overall plant health. These insights carry notable implications for future studies, particularly those focused on the endophytes of PG and their secondary metabolites, as they deepen our understanding of plant-microbe interactions and their role in enhancing the plants' therapeutic potential.

From grasslands to genes: exploring the major microbial drivers of antibiotic-resistance in microhabitats under persistent overgrazing

BACKGROUND

The extensive use of antibiotics in the global livestock industry in recent decades has accelerated the accumulation and dissemination of antibiotic-resistance genes (ARGs) within terrestrial ecosystems. This occurs due to the limited absorption of most antibiotics, leading to their release into the environment through feces and urine. This poses a significant threat to both the environment and human health. However, the response of antibiotic-resistant microorganisms and their ARGs in grasslands to prolonged grazing, as well as the primary microbial taxa driving the ARG distribution, remain poorly understood, especially within various microhabitats. In this study, we characterized ARGs in the phyllosphere, litter, and soil after decades of livestock grazing in a meadow steppe. We particularly focused on identifying the major members of the microbial community influencing ARGs and the distinction between microbial generalists and specialists.

RESULTS

Our findings indicate that a core set of ARGs accounted for 90% of the abundance in this plant-soil ecosystem. While the soil exhibited the highest ARG abundance, the phyllosphere, and litter displayed higher ARG diversity and diverse distribution patterns after overgrazing. Grazing increased ARG abundance by elevating the proportion of core ARGs and suppressing stochastic ARGs in the phyllosphere and litter, while it had little effect on the ARGs in the soil. Additionally, microbial generalist abundance increased, but specialist abundance decreased in the phyllosphere and litter, with no effect in the soil, under grazed conditions. Ultimately, microbial microhabitats and grazing influenced ARG community characteristics through direct (i.e., feces and other exogenous ARG input) and indirect (i.e., trampling and selective feeding) effects on nutrient availability, microbial community composition, and mobile genetic elements. The generalist community, with its broad ecological niches and phylogenetic composition, made the most significant contribution to the ARG characteristics.

CONCLUSIONS

This study underscores the impact of environmental disturbances on the distributional patterns of ARGs in ecosystems, mediated by the regulation of microbial generalized species. These insights enhance our understanding of microbial control over ARGs and facilitate predictions regarding the dynamics and risk of ARGs in diverse ecological niches subjected to anthropogenic disturbances. Video Abstract.

Divergence and convergence in epiphytic and endophytic phyllosphere bacterial communities of rice landraces

Phyllosphere-associated microbes can significantly alter host plant fitness, with distinct functions provided by bacteria inhabiting the epiphytic (external surface) vs endophytic niches (internal leaf tissue). Hence, it is important to understand the assembly and stability of these phyllosphere communities, especially in field conditions. Broadly, epiphytic communities should encounter more environmental fluctuations and frequent immigration, whereas endophytic microbiota should face stronger host selection. As a result, we expect greater variability in epiphytic than endophytic communities. We analyzed the structure and stability of leaf phyllosphere microbiota of four traditionally cultivated rice landraces and one commercial variety from northeast India grown in the field for 3 consecutive years, supplemented with opportunistic sampling of eight other landraces. Epiphytic and endophytic bacterial communities shared dominant core genera such as Methylobacterium and Sphingomonas. Consistent with an overall strong environmental effect, both communities varied more across sampling years than across host landraces. Seeds sampled from a focal landrace did not support vertical transmission of phyllosphere bacteria, suggesting that both types of communities are assembled anew each generation. Despite these points of convergence, epiphytic communities had distinct composition and significantly higher microbial load and were more rich, diverse, modular, and unstable than endophytic communities. Finally, focused sampling of one landrace across developmental stages showed that the divergence between the two types of communities arose primarily at the flowering stage. Thus, our results show both convergent and divergent patterns of community assembly and composition in distinct phyllosphere niches in rice, identifying key bacterial genera and host developmental stages that may aid agricultural interventions to increase rice yield.IMPORTANCEPhyllosphere (leaf-associated) microbes significantly impact plant fitness, making it crucial to understand how these communities are assembled and maintained. While many studies have analyzed epiphytic (surface) phyllosphere communities, we have a relatively poor understanding of endophytic communities which colonize the very distinct niche formed inside leaf tissues. We found that across several rice landraces, both communities are largely colonized by the same core genera, indicating divergence at the species level across the two leaf niches and highlighting the need to understand the mechanisms underlying this divergence. Surprisingly, both epiphytic and endophytic communities were only weakly shaped by the host landrace, with a much greater role for environmental factors that likely vary over time. Thus, microbiome-based agricultural interventions for increasing productivity could perhaps be generalized across rice varieties but would need to account for the temporal instability of the microbiota. Our results thus highlight the importance of data sets such as ours-with extensive sampling across landraces and years-for understanding phyllosphere microbiota and their applications in the field.

Tissue ontogeny and chemical composition influence bacterial biodiversity in the wood and shoot tip of Populus nigra

Plant-microbe interactions significantly influence plant growth dynamics and adaptability. This study explores the impact of metabolites on microbial biodiversity in shoot tips and wood of Populus nigra under greenhouse conditions, using high-throughput sequencing and metabolite profiling. Branches from P. nigra were harvested, rooted, and transplanted into pots for growth. After 3 months, tissue samples from shoot tips and wood were collected, and metabolites extracted and analysed using GC-MS and LC-MS. Genomic DNA was extracted and subjected to high-throughput sequencing for bacterial biodiversity profiling. Both datasets were analysed using bioinformatic and statistical pipelines. Metabolite profiling indicated that shoot tips had a higher relative abundance of primary and secondary metabolites, including sugars, fatty acids, organic acids, phenolic acid derivatives and salicinoids, while wood was enriched in flavonoids. Bacterial biodiversity also differed significantly between these tissues, with Clostridiales, Bacteroidales and Bacillales dominating in shoot tips, associated with rapid growth and anaerobic fermentation, while wood tissues were characterized by diazotrophs from Rhizobiales, Sphingomonadales and Frankiales. PCoA clustering confirmed tissue-specific microbial differences. Functional analysis revealed an enrichment of fundamental cellular processes in shoot tips, while wood exhibited pathways related to degradation and mortality. Metabolite profiling revealed significant variations in primary and secondary metabolites, highlighting their influence on microbial biodiversity across plant tissues. The dominance of specific bacterial orders and distinct functional pathways in each tissue suggests a tailored microbial response to the unique environments of shoot tips and wood.

Glucosinolate structural diversity shapes recruitment of a metabolic network of leaf-associated bacteria

Host defenses can have broader ecological roles, but how they shape natural microbiome recruitment is poorly understood. Aliphatic glucosinolates (GLSs) are secondary defense metabolites in Brassicaceae plant leaves. Their genetically defined structure shapes interactions with pests in Arabidopsis thaliana leaves, and here we find that it also shapes bacterial recruitment. In model genotype Col-0, GLSs (mostly 4-methylsulfinylbutyl-GLS) have no clear effect on natural leaf bacterial recruitment. In a genotype from a wild population, however, GLSs (mostly allyl-GLS) enrich specific taxa, mostly Comamonadaceae and Oxalobacteraceae. Consistently, Comamonadaceae are also enriched in wild A. thaliana, and Oxalobacteraceae are enriched from wild plants on allyl-GLS as carbon source, but not on 4-methylsulfinylbutyl-GLS. Recruitment differences between GLS structures most likely arise from bacterial myrosinase specificity. Community recruitment is then defined by metabolic cross-feeding among bacteria. The link of genetically defined metabolites to recruitment could lead to new strategies to shape plant microbiome balance.

Time of arrival during plant disease progression and humidity additively influence Salmonella enterica colonization of lettuce

The interplay between plant hosts, phytopathogenic bacteria, and enteric human pathogens in the phyllosphere has consequences for human health. Salmonella enterica has been known to take advantage of phytobacterial infection to increase its success on plants, but there is little knowledge of additional factors that may influence the relationship between enteric pathogens and plant disease. In this study, we investigated the role of humidity and the extent of plant disease progression on S. enterica colonization of plants. We found that high humidity was necessary for the replication of S. enterica on diseased lettuce, but not required for S. enterica ingress into the UV-protected apoplast. Additionally, the Xanthomonas hortorum pv. vitians (hereafter, X. vitians)-infected lettuce host was found to be a relatively hostile environment for S. enterica when it arrived prior to the development of watersoaking or following necrosis onset, supporting the existence of an ideal window during X. vitians infection progress that maximizes S. enterica survival. In vitro growth studies in sucrose media suggest that X. vitians may allow S. enterica to benefit from cross-feeding during plant infection. Overall, this study emphasizes the role of phytobacterial disease as a driver of S. enterica success in the phyllosphere, demonstrates how the time of arrival during disease progress can influence S. enterica's fate in the apoplast, and highlights the potential for humidity to transform an infected apoplast into a growth-promoting environment for bacterial colonizers.

IMPORTANCE

Bacterial leaf spot of lettuce caused by Xanthomonas hortorum pv. vitians is a common threat to leafy green production. The global impact caused by phytopathogens, including X. vitians, is likely to increase with climate change. We found that even under a scenario where increased humidity did not enhance plant disease, high humidity had a substantial effect on facilitating Salmonella enterica growth on Xanthomonas-infected plants. High humidity climates may directly contribute to the survival of human enteric pathogens in crop fields or indirectly affect bacterial survival via changes to the phyllosphere brought on by phytopathogen disease.

Health by design; optimising our urban environmental microbiomes for human health

Humans have evolved in direct and intimate contact with their environment and the microbes that it contains, over a period of 2 million years. As a result, human physiology has become intrinsically linked to environmental microbiota. Urbanisation has reduced our exposure to harmful pathogens, however there is now increasing evidence that these same health-protective improvements in our environment may also be contributing to a hidden disease burden: immune dysregulation. Thoughtful and purposeful design has the potential to ameliorate these health concerns by providing sources of microbial diversity for human exposure. In this narrative review, we highlight the role of environmental microbiota in human health and provide insights into how we can optimise human health through well-designed cities, urban landscapes and buildings. The World Health Organization recommends there should be at least one public green space of least 0.5 ha in size within 300m of a place of residence. We argue that these larger green spaces are more likely to permit functioning ecosystems that deliver ecosystem services, including the provision of diverse aerobiomes. Urban planning must consider the conservation and addition of large public green spaces, while landscape design needs to consider how to maximise environmental, social and public health outcomes, which may include rewilding. Landscape designers need to consider how people use these spaces, and how to optimise utilisation, including for those who may experience challenges in access (e.g. those living with disabilities, people in residential care). There are also opportunities to improve health via building design that improves access to diverse environmental microbiota. Considerations include having windows that open, indoor plants, and the relationship between function, form and organization. We emphasise possibilities for re-introducing potentially health-giving microbial exposures into urban environments, particularly where the benefits of exposure to biodiverse environments may have been lost.

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.

Urban greenspace types and climate factors jointly drive the microbial community structure and co-occurrence network

The benefits of urban green space are socially widely recognized as a direct link between plant-microbe interactions and the maintenance of biodiversity, community stability, and ecosystem functioning. Nevertheless, there is a lack of knowledge about the factors influencing microbial communities in urban green spaces, especially those related to phyllosphere epiphytes and stem epiphytes. In this study, we analyzed the microbial community assembly in leaf and stem bark samples collected from Square, Road, Campus, and Park. Illumina sequecing of 16S amplicons was performed to characterize microbial diversity and composition. The α-diversity was significantly higher in the bark epiphytic community, compared to the phyllosphere. Moreover, urban greenspaces'type altered the way communities gathered. The main soil and air properties factors of the urban greenhouse (e.g. soil temperature, atmospheric moisture, air temperature) were shaping the characteristics of bacterial communities on the leaf surface and bark epiphytic. In addition, in the co-occurrence network analysis, keystone taxa were not mostly observed in abundant species, which may be necessary to maintain ecosystem functions. Finally, our findings provide a deeper understanding of the ecological dynamics and microbial interactions within plant phyllosphere and stem epiphytes microbiomes.

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.

Global insights into endophytic bacterial communities of terrestrial plants: Exploring the potential applications of endophytic microbiota in sustainable agriculture

Endophytic microorganisms are indispensable symbionts during plant growth and development and often serve functions such as growth promotion and stress resistance in plants. Therefore, an increasing number of researchers have applied endophytes for multifaceted phytoremediation (e.g., organic pollutants and heavy metals) in recent years. With the availability of next-generation sequencing technologies, an increasing number of studies have shifted the focus from culturable bacteria to total communities. However, information on the composition, structure, and function of bacterial endophytic communities is still not widely synthesized. To explore the general patterns of variation in bacterial communities between plant niches, we reanalyzed data from 1499 samples in 30 individual studies from different continents and provided comprehensive insights. A group of bacterial genera were commonly found in most plant roots and shoots. Our analysis revealed distinct variations in the diversity, composition, structure, and function of endophytic bacterial communities between plant roots and shoots. These variations underscore the sophisticated mechanisms by which plants engage with their endophytic microbiota, optimizing these interactions to bolster growth, health, and resilience against stress. Highlighting the strategic role of endophytic bacteria in promoting sustainable agricultural practices and environmental stewardship, our study not only offers global insights into the endophytic bacterial communities of terrestrial plants but also underscores the untapped potential of these communities as invaluable resources for future research.

Hitching a Ride in the Phyllosphere: Surfactant Production of Pseudomonas spp. Causes Co-swarming of Pantoea eucalypti 299R

Here, we demonstrate the beneficial effect of surfactant-producing pseudomonads on Pantoea eucalypti 299R. We conducted a series of experiments in environments of increasing complexity. P. eucalypti 299R (Pe299R), and Pseudomonas sp. FF1 (Pff1) or Pe299R and surfactant-production deficient Pseudomonas sp. FF1::ΔviscB (Pff1ΔviscB) were co-inoculated in broth, on swarming agar plates, and on plants. In broth, there were no differences in the growth dynamics of Pe299R when growing in the presence of Pff1 or Pff1ΔviscB. By contrast, on swarming agar plates, Pe299R was able to co-swarm with Pff1 which led to a significant increase in Pe299R biomass compared to Pe299R growing with Pff1ΔviscB or in monoculture. Finally in planta, and using the single-cell bioreporter for reproductive success (CUSPER), we found a temporally distinct beneficial effect of Pff1 on co-inoculated Pe299R subpopulations that did not occur in the presence of Pff1ΔviscB. We tested three additional surfactant-producing pseudomonads and their respective surfactant knockout mutants on PE299R on swarming agar showing similar results. This led us to propose a model for the positive effect of surfactant production during leaf colonization. Our results indicate that co-motility might be common during leaf colonization and adds yet another facet to the already manyfold roles of surfactants.

Powdery mildew-induced changes in phyllosphere microbial community dynamics of cucumber

As an important habitat for microorganisms, the phyllosphere has a great impact on plant growth and health, and changes in phyllosphere microorganisms are closely related to the occurrence of leaf diseases. However, there remains a limited understanding regarding alterations to the microbial community in the phyllosphere resulting from pathogen infections. Here, we analyzed and compared the differences in phyllosphere microorganisms of powdery mildew cucumber from three disease severity levels (0% < L1 < 30%, 30% ≤ L2 < 50%, L3 ≥ 50%, the number represents the lesion coverage rate of powdery mildew on leaves). There were significant differences in α diversity and community structure of phyllosphere communities under different disease levels. Disease severity altered the community structure of phyllosphere microorganisms, Rosenbergiella, Rickettsia, and Cladosporium accounted for the largest proportion in the L1 disease grade, while Bacillus, Pantoea, Kocuria, and Podosphaera had the highest relative abundance in the L3 disease grade. The co-occurrence network analysis of the phyllosphere microbial community indicated that the phyllosphere bacterial community was most affected by the severity of disease. Our results suggested that with the development of cucumber powdery mildew, the symbiotic relationship between species was broken, and the entire bacterial community tended to compete.

Nonpathogenic leaf-colonizing bacteria elicit pathogen-like responses in a colonization density-dependent manner

Leaves are colonized by a complex mix of microbes, termed the leaf microbiota. Even though the leaf microbiota is increasingly recognized as an integral part of plant life and health, our understanding of its interactions with the plant host is still limited. Here, mature, axenically grown Arabidopsis thaliana plants were spray inoculated with six diverse leaf-colonizing bacteria. The transcriptomic changes in leaves were tracked over time and significant changes in ethylene marker (ARL2) expression were observed only 2-4 days after spray inoculation. Whole-transcriptome sequencing revealed that 4 days after inoculation, leaf transcriptional changes to colonization by nonpathogenic and pathogenic bacteria differed in strength but not in the type of response. Inoculation of plants with different densities of the nonpathogenic bacterium Williamsia sp. Leaf354 showed that high bacterial titers resulted in disease phenotypes and led to severe transcriptional reprogramming with a strong focus on plant defense. An in silico epigenetic analysis of the data was congruent with the transcriptomic analysis. These findings suggest (1) that plant responses are not rapid after spray inoculation, (2) that plant responses only differ in strength, and (3) that plants respond to high titers of nonpathogenic bacteria with pathogen-like responses.

A scientific version of understanding "Why did the chickens cross the road"? - A guided journey through Bacillus spp. towards sustainable agriculture, circular economy and biofortification

The world, a famished planet with an overgrowing population, requires enormous food crops. This scenario compelled the farmers to use a high quantity of synthetic fertilizers for high food crop productivity. However, prolonged usage of chemical fertilizers results in severe adverse effects on soil and water quality. On the other hand, the growing population significantly consumes large quantities of poultry meats. Eventually, this produces a mammoth amount of poultry waste, chicken feathers. Owing to the protein value of the chicken feathers, these wastes are converted into protein hydrolysate and further extend their application as biostimulants for sustained agriculture. The protein profile of chicken feather protein hydrolysate (CFPH) produced through Bacillus spp. was the maximum compared to physical and chemical protein extraction methods. Several studies proved that the application of CFPH and active Bacillus spp. culture to soil and plants results in enhanced plant growth, phytochemical constituents, crop yield, soil nutrients, fertility, microbiome and resistance against diverse abiotic and biotic stresses. Overall, "CFPH - Jack of all trades" and "Bacillus spp. - an active camouflage to the surroundings where they applied showed profound and significant benefits to the plant growth under the most adverse conditions. In addition, Bacillus spp. coheres the biofortification process in plants through the breakdown of metals into metal ions that eventually increase the nutrient value of the food crops. However, detailed information on them is missing. This can be overcome by further real-world studies on rhizoengineering through a multi-omics approach and their interaction with plants. This review has explored the best possible and efficient strategy for managing chicken feather wastes into protein-rich CFPH through Bacillus spp. bioconversion and utilizing the CFPH and Bacillus spp. as biostimulants, biofertilizers, biopesticides and biofortificants. This paper is an excellent report on organic waste management, circular economy and sustainable agriculture research frontier.

Temporal variations of antimicrobial resistance genes in aerosols: A one-year monitoring at the puy de Dôme summit (Central France)

The recent characterization of antibiotic resistance genes (ARGs) in clouds evidenced that the atmosphere actively partakes in the global spreading of antibiotic resistance worldwide. Indeed, the outdoor atmosphere continuously receives large quantities of particles of biological origins, emitted from both anthropogenic or natural sources at the near Earth's surface. Nonetheless, our understanding of the composition of the atmospheric resistome, especially at mid-altitude (i.e. above 1000 m a.s.l.), remains largely limited. The atmosphere is vast and highly dynamic, so that the diversity and abundance of ARGs are expected to fluctuate both spatially and temporally. In this work, the abundance and diversity of ARGs were assessed in atmospheric aerosol samples collected weekly between July 2016 and August 2017 at the mountain site of puy de Dôme (1465 m a.s.l., central France). Our results evidence the presence of 33 different subtypes of ARGs in atmospheric aerosols, out of 34 assessed, whose total concentration fluctuated seasonally from 59 to 1.1 × 105 copies m-3 of air. These were heavily dominated by genes from the quinolone resistance family, notably the qepA gene encoding efflux pump mechanisms, which represented >95 % of total ARGs concentration. Its abundance positively correlated with that of bacteria affiliated with the genera Kineococcus, Neorhizobium, Devosia or Massilia, ubiquitous in soils. This, along with the high abundance of Sphingomonas species, points toward a large contribution of natural sources to the airborne ARGs. Nonetheless, the increased contribution of macrolide resistance (notably the erm35 gene) during winter suggests a sporadic diffusion of ARGs from human activities. Our observations depict the atmosphere as an important vector of ARGs from terrestrial sources. Therefore, monitoring ARGs in airborne microorganisms appears necessary to fully understand the dynamics of antimicrobial resistances in the environment and mitigate the threats they may represent.

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.

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

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

Temporal variations in reactive oxygen species in biofilms of submerged macrophytes: The key role of microbial metabolism mediated by oxygen fluctuations

Reactive oxygen species (ROS) play a crucial role in the biogeochemistry of aquatic environments, yet their occurrence and accumulation in the biofilm of submerged macrophytes have been poorly documented. Herein, we first investigated the light-dark cycling fluctuations of biofilm microenvironment and the temporal variations of a representative ROS (O2•-) during biofilm succession on the macrophyte leaves and subsequently quantified the photochemical processes in biofilms. The sustained production of O2•- exhibited a distinct rhythmic fluctuation from 32.49 ± 0.56 μmol/kg to 72.56 ± 0.92 μmol/kg FW, which simultaneously fluctuated with the dissolved oxygen, redox potential, and pH, all driven by the alternating oxic-anoxic conditions of biofilms. The intensities of O2•- and ROS firstly increased and then decreased throughout biofilm succession. The O2•- concentrations in biofilms from different waters followed the order of rural river water > landscape lake water > aquaculture pond water, and the leaf photosynthesis and microbial community played a key role. ROS production was significantly associated with Actinobacteria, Proteobacteria and Bacteroidetes, with contributions of 44.6%, 32.8%, and 15.2%, respectively. Partial least squares path modeling structural equation analysis showed that ROS production in leaf biofilms was mainly related to the microenvironment and microbial metabolism. These findings will facilitate the development of ecological restoration strategies in aquatic environments.

Microbial communities living inside plant leaves or on the leaf surface are differently shaped by environmental cues

Leaf-associated microbial communities can promote plant health and resistance to biotic and abiotic stresses. However, the importance of environmental cues in the assembly of the leaf endo- and epi-microbiota remains elusive. Here, we aimed to investigate the impact of seasonal environmental variations, on the establishment of the leaf microbiome, focusing on long-term changes (five years) in bacterial, fungal, and nonfungal eukaryotic communities colonizing the surface and endosphere of six wild Arabidopsis thaliana populations. While leaf-microbial communities were found to be highly stochastic, the leaf niche had a predominant importance with endophytic microbial communities consistently exhibiting a lower diversity and variability. Among environmental factors, radiation- and humidity-related factors are the most important drivers of diversity patterns in the leaf, with stronger effects on epiphytic communities. Using linear models, we identified 30 important genera whose relative abundance in leaf compartments could be modeled from environmental variables, suggesting specific niche preferences for these taxa. With the hypothesis that environmental factors could impact interactions within microbial communities, we analyzed the seasonal patterns of microbial interaction networks across leaf compartments. We showed that epiphytic networks are more complex than endophytic and that the complexity and connectivity of these networks are partially correlated with the mentioned environmental cues. Our results indicate that humidity and solar radiation function as major environmental cues shaping the phyllosphere microbiome at both micro (leaf compartment) and macro (site) scales. These findings could have practical implications for predicting and developing field-adapted microbes in the face of global change.

Linking ecological niches to bacterial community structure and assembly in polluted urban aquatic ecosystems

Introduction

Bacterial communities play crucial roles in the functioning and resilience of aquatic ecosystems, and their responses to water pollution may be assessed from ecological niches. However, our understanding of such response patterns and the underlying ecological mechanisms remains limited.

Methods

In this study, we comprehensively investigated the effects of water pollution on the bacterial structure and assembly within different ecological niches, including water, sediment, submerged plant leaf surfaces, and leaf surfaces, using a 16S high-throughput sequencing approach.

Results

Ecological niches had a greater impact on bacterial community diversity than pollution, with a distinct enrichment of unique dominant phyla in different niches. This disparity in diversity extends to the bacterial responses to water pollution, with a general reduction in α-diversity observed in the niches, excluding leaf surfaces. Additionally, the distinct changes in bacterial composition in response to pollution should be correlated with their predicted functions, given the enrichment of functions related to biogeochemical cycling in plant surface niches. Moreover, our study revealed diverse interaction patterns among bacterial communities in different niches, characterized by relatively simply associations in sediments and intricate or interconnected networks in water and plant surfaces. Furthermore, stochastic processes dominated bacterial community assembly in the water column, whereas selective screening of roots and pollution events increased the impact of deterministic processes.

Discussion

Overall, our study emphasizes the importance of ecological niches in shaping bacterial responses to water pollution. These findings improve our understanding of the complicated microbial response patterns to water pollution and have ecological implications for aquatic ecosystem health.

The Relationship between the Sugar Preference of Bacterial Pathogens and Virulence on Plants

Plant pathogenic bacteria colonize plant surfaces and inner tissues to acquire essential nutrients. Nonstructural sugars hold paramount significance among these nutrients, as they serve as pivotal carbon sources for bacterial sustenance. They obtain sugar from their host by diverting nonstructural carbohydrates en route to the sink or enzymatic breakdown of structural carbohydrates within plant tissues. Despite the prevalence of research in this domain, the area of sugar selectivity and preferences exhibited by plant pathogenic bacteria remains inadequately explored. Within this expository framework, our present review endeavors to elucidate the intricate variations characterizing the distribution of simple sugars within diverse plant tissues, thus influencing the virulence dynamics of plant pathogenic bacteria. Subsequently, we illustrate the apparent significance of comprehending the bacterial preference for specific sugars and sugar alcohols, postulating this insight as a promising avenue to deepen our comprehension of bacterial pathogenicity. This enriched understanding, in turn, stands to catalyze the development of more efficacious strategies for the mitigation of plant diseases instigated by bacterial pathogens.

Tillandsia landbeckii phyllosphere and laimosphere as refugia for bacterial life in a hyperarid desert environment

BACKGROUND

The lack of water is a major constraint for microbial life in hyperarid deserts. Consequently, the abundance and diversity of microorganisms in common habitats such as soil are strongly reduced, and colonization occurs primarily by specifically adapted microorganisms that thrive in particular refugia to escape the harsh conditions that prevail in these deserts. We suggest that plants provide another refugium for microbial life in hyperarid deserts. We studied the bacterial colonization of Tillandsia landbeckii (Bromeliaceae) plants, which occur in the hyperarid regions of the Atacama Desert in Chile, one of the driest and oldest deserts on Earth.

RESULTS

We detected clear differences between the bacterial communities being plant associated to those of the bare soil surface (PERMANOVA, R2 = 0.187, p = 0.001), indicating that Tillandsia plants host a specific bacterial community, not only dust-deposited cells. Moreover, the bacterial communities in the phyllosphere were distinct from those in the laimosphere, i.e., on buried shoots (R2 = 0.108, p = 0.001), indicating further habitat differentiation within plant individuals. The bacterial taxa detected in the phyllosphere are partly well-known phyllosphere colonizers, but in addition, some rather unusual taxa (subgroup2 Acidobacteriae, Acidiphilum) and insect endosymbionts (Wolbachia, "Candidatus Uzinura") were found. The laimosphere hosted phyllosphere-associated as well as soil-derived taxa. The phyllosphere bacterial communities showed biogeographic patterns across the desert (R2 = 0.331, p = 0.001). These patterns were different and even more pronounced in the laimosphere (R2 = 0.467, p = 0.001), indicating that different factors determine community assembly in the two plant compartments. Furthermore, the phyllosphere microbiota underwent temporal changes (R2 = 0.064, p = 0.001).

CONCLUSIONS

Our data demonstrate that T. landbeckii plants host specific bacterial communities in the phyllosphere as well as in the laimosphere. Therewith, these plants provide compartment-specific refugia for microbial life in hyperarid desert environments. The bacterial communities show biogeographic patterns and temporal variation, as known from other plant microbiomes, demonstrating environmental responsiveness and suggesting that bacteria inhabit these plants as viable microorganisms. Video Abstract.

The Cultured Microbiome of Pollinated Maize Silks Shifts after Infection with Fusarium graminearum and Varies by Distance from the Site of Pathogen Inoculation

Styles transmit pollen-derived sperm nuclei from pollen to ovules, but also transmit environmental pathogens. The microbiomes of styles are likely important for reproduction/disease, yet few studies exist. Whether style microbiome compositions are spatially responsive to pathogens is unknown. The maize pathogen Fusarium graminearum enters developing grain through the style (silk). We hypothesized that F. graminearum treatment shifts the cultured transmitting silk microbiome (TSM) compared to healthy silks in a distance-dependent manner. Another objective of the study was to culture microbes for future application. Bacteria were cultured from husk-covered silks of 14 F. graminearum-treated diverse maize genotypes, proximal (tip) and distal (base) to the F. graminearum inoculation site. Long-read 16S sequences from 398 isolates spanned 35 genera, 71 species, and 238 OTUs. More bacteria were cultured from F. graminearum-inoculated tips (271 isolates) versus base (127 isolates); healthy silks were balanced. F. graminearum caused a collapse in diversity of ~20-25% across multiple taxonomic levels. Some species were cultured exclusively or, more often, from F. graminearum-treated silks (e.g., Delftia acidovorans, Klebsiella aerogenes, K. grimontii, Pantoea ananatis, Stenotrophomonas pavanii). Overall, the results suggest that F. graminearum alters the TSM in a distance-dependent manner. Many isolates matched taxa that were previously identified using V4-MiSeq (core and F. graminearum-induced), but long-read sequencing clarified the taxonomy and uncovered greater diversity than was initially predicted (e.g., within Pantoea). These isolates represent the first comprehensive cultured collection from pathogen-treated maize silks to facilitate biocontrol efforts and microbial marker-assisted breeding.

Distinct patterns of the soil and phyllosphere antibiotic resistome in natural forest ecosystems under an altitudinal gradient

Warming affects microbial functioning of soil and the phyllosphere across global ecosystems. However, little is known about the impact of increasing temperature on antibiotic resistome profiles in natural forests. To address this issue, we investigated antibiotic resistance genes (ARGs) in both soil and the plant phyllosphere using an experimental platform established in a forest ecosystem that delivers a temperature difference of 2.1 °C along an altitudinal gradient. Principal Coordinate Analysis (PCoA) showed that there were significant differences in the composition of soil and plant phyllosphere ARGs at different altitudes (P = 0.001). The relative abundance of phyllosphere ARGs and mobile genetic elements (MGEs) and soil MGEs increased with temperature. More resistance gene classes increased in abundance in the phyllosphere (10 classes) than soil (2 classes), and a Random Forest model analysis suggested that phyllosphere ARGs were more sensitive to temperature change than soil. Increasing temperature as a direct consequence of an altitudinal gradient, and the relative abundance of MGEs were the main drivers that shaped the profiles of ARGs in the phyllosphere and soil. Biotic and abiotic factors affected phyllosphere ARGs indirectly via MGEs. This study enhances our understanding of the influence of altitude gradients on resistance genes in natural environments.

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.

Harmonized biochemical modification of cell walls to get permission for entrance of Azospirillum sp. to rice roots

Biological nitrogen-fixation is important in increasing crop efficiency. Azospirillum is a nitrogen-fixing microorganism that naturally coexists with grasses roots. The present study was undertaken to clarify the role of rice root cell walls in the acceptance of two Azospirillum species, alone or in combination with indole-3-acetic acid (IAA) and gibberellic acid (GA3) treatments. Rice seedlings were grown in Yoshida solution for 21 days and then inoculated with A. brasilense and A. irakens in the presence of 0, 0.57, and 1.14 mM of IAA or 0, 0.29, and 0.58 mM GA3 or a combination of 1.14 mM of IAA and 0.58 mM of GA3. The results showed that the amount of hydrogen peroxide, lipid peroxidation, total nitrogen and activity of ferulic acid peroxidase, NADPH oxidase, nitrate reductase, pectin methyl esterase, cellulase, mannanase, xylanase and pectinase were significantly increased in inoculated samples treated with or without phytohormones. The highest activity of these enzymes was observed in A. brasilense- inoculated rice roots in auxin+gibberellin treatment. In the latter, the activity of phenylalanine ammonia lyase and wall ferulic acid peroxidase enzymes, the content of cell wall polysaccharide, lignin, and total phenolic compounds were the least, compared to controls and also with those samples which were inoculated with A. irakens. The results indicate an active role of the wall and its enzymes in allowing bacteria to enter the roots. Understanding this mechanism can improve the methods of inoculating bacteria into plants and increase crop efficiency, which will result in reduced use of chemical fertilizers and their destructive environmental effects.

Current Scenario and Future Prospects of Endophytic Microbes: Promising Candidates for Abiotic and Biotic Stress Management for Agricultural and Environmental Sustainability

Globally, substantial research into endophytic microbes is being conducted to increase agricultural and environmental sustainability. Endophytic microbes such as bacteria, actinomycetes, and fungi inhabit ubiquitously within the tissues of all plant species without causing any harm or disease. Endophytes form symbiotic relationships with diverse plant species and can regulate numerous host functions, including resistance to abiotic and biotic stresses, growth and development, and stimulating immune systems. Moreover, plant endophytes play a dominant role in nutrient cycling, biodegradation, and bioremediation, and are widely used in many industries. Endophytes have a stronger predisposition for enhancing mineral and metal solubility by cells through the secretion of organic acids with low molecular weight and metal-specific ligands (such as siderophores) that alter soil pH and boost binding activity. Finally, endophytes synthesize various bioactive compounds with high competence that are promising candidates for new drugs, antibiotics, and medicines. Bioprospecting of endophytic novel secondary metabolites has given momentum to sustainable agriculture for combating environmental stresses. Biotechnological interventions with the aid of endophytes played a pivotal role in crop improvement to mitigate biotic and abiotic stress conditions like drought, salinity, xenobiotic compounds, and heavy metals. Identification of putative genes from endophytes conferring resistance and tolerance to crop diseases, apart from those involved in the accumulation and degradation of contaminants, could open new avenues in agricultural research and development. Furthermore, a detailed molecular and biochemical understanding of endophyte entry and colonization strategy in the host would better help in manipulating crop productivity under changing climatic conditions. Therefore, the present review highlights current research trends based on the SCOPUS database, potential biotechnological interventions of endophytic microorganisms in combating environmental stresses influencing crop productivity, future opportunities of endophytes in improving plant stress tolerance, and their contribution to sustainable remediation of hazardous environmental contaminants.

Rhizobiome Transplantation: A Novel Strategy beyond Single-Strain/Consortium Inoculation for Crop Improvement

The growing human population has a greater demand for food; however, the care and preservation of nature as well as its resources must be considered when fulfilling this demand. An alternative employed in recent decades is the use and application of microbial inoculants, either individually or in consortium. The transplantation of rhizospheric microbiomes (rhizobiome) recently emerged as an additional proposal to protect crops from pathogens. In this review, rhizobiome transplantation was analyzed as an ecological alternative for increasing plant protection and crop production. The differences between single-strain/species inoculation and dual or consortium application were compared. Furthermore, the feasibility of the transplantation of other associated micro-communities, including phyllosphere and endosphere microbiomes, were evaluated. The current and future challenges surrounding rhizobiome transplantation were additionally discussed. In conclusion, rhizobiome transplantation emerges as an attractive alternative that goes beyond single/group inoculation of microbial agents; however, there is still a long way ahead before it can be applied in large-scale agriculture.

Epiphytic microbiota in Swedish grass-clover herbage and the effect of silage additives on fermentation profiles and bacterial community compositions of the resulting silages

AIMS

To investigate the epiphytic microbiota in grass-clover herbage harvested at different sites and occasions and to explore the effect of different silage additives on the resulting silage microbiota.

METHODS AND RESULTS

Herbage was harvested from grass-clover leys at geographically distributed sites in a long-term field experiment in Sweden, in early and late season of two consecutive years. Different silages were made from the herbage using: (1) no additive, (2) acid-treatment, and (3) inoculation by starter culture. Herbages were analysed for botanical and chemical composition, and the resulting silages for products of fermentation. Bacterial DNA was extracted from herbage and silage samples, followed by sequencing using Illumina 16S rRNA amplicon sequencing. Herbage microbiota showed no clear correlation to site or harvesting time. Silage additives had a major effect on the ensiling process; inoculation resulted in well fermented silages comprising a homogenous microbiota dominated by the genera Lactobacillus and Pediococcus. A minor effect of harvest time was also observed, with generally a more diverse microbiota in second-harvest silages. Untreated silages showed a higher relative abundance (RA) from non-lactic acid bacteria compared to acid-treated silages. In most silages, only a few bacterial amplicon sequence variants contributed to most of the RA.

CONCLUSIONS

The epiphytic microbiota in grass-clover herbage were found to be random and not dependent on site. From a microbial point of view, the most predictable and preferable silage outcome was obtained by inoculation with a starter culture. Acid-treatment with formic- and propionic acid surprisingly resulted in a less preferable silage. Silage making without additives cannot be recommended based on our results.

Inter- and intraspecific phytochemical variation correlate with epiphytic flower and leaf bacterial communities

Microbes associated with flowers and leaves affect plant health and fitness and modify the chemical phenotypes of plants with consequences for interactions of plants with their environment. However, the drivers of bacterial communities colonizing above-ground parts of grassland plants in the field remain largely unknown. We therefore examined the relationships between phytochemistry and the epiphytic bacterial community composition of flowers and leaves of Ranunculus acris and Trifolium pratense. On 252 plant individuals, we characterized primary and specialized metabolites, that is, surface sugars, volatile organic compounds (VOCs), and metabolic fingerprints, as well as epiphytic flower and leaf bacterial communities. The genomic potential of bacterial colonizers concerning metabolic capacities was assessed using bacterial reference genomes. Phytochemical composition displayed pronounced variation within and between plant species and organs, which explained part of the variation in bacterial community composition. Correlation network analysis suggests strain-specific correlations with metabolites. Analysis of bacterial reference genomes revealed taxon-specific metabolic capabilities that corresponded with genes involved in glycolysis and adaptation to osmotic stress. Our results show relationships between phytochemistry and the flower and leaf bacterial microbiomes suggesting that plants provide chemical niches for distinct bacterial communities. In turn, bacteria may induce alterations in the plants' chemical phenotype. Thus, our study may stimulate further research on the mechanisms of trait-based community assembly in epiphytic bacteria.

Metabolic resource overlap impacts competition among phyllosphere bacteria

The phyllosphere is densely colonised by microbial communities, despite sparse and heterogeneously distributed resources. The limitation of resources is expected to drive bacterial competition resulting in exclusion or coexistence based on fitness differences and resource overlap between individual colonisers. We studied the impact of resource competition by determining the effects of different bacterial colonisers on the growth of the model epiphyte Pantoea eucalypti 299R (Pe299R). Resource overlap was predicted based on genome-scale metabolic modelling. By combining results of metabolic modelling and pairwise competitions in the Arabidopsis thaliana phyllosphere and in vitro, we found that ten resources sufficed to explain fitness of Pe299R. An effect of both resource overlap and phylogenetic relationships was found on competition outcomes in vitro as well as in the phyllosphere. However, effects of resource competition were much weaker in the phyllosphere when compared to in vitro experiments. When investigating growth dynamics and reproductive success at the single-cell resolution, resource overlap and phylogenetic relationships are only weakly correlated with epiphytic Pe299R reproductive success, indicating that the leaf's spatial heterogeneity mitigates resource competition. Although the correlation is weak, the presence of competitors led to the development of Pe299R subpopulations that experienced different life histories and cell divisions. In some in planta competitions, Pe299R benefitted from the presence of epiphytes despite high resource overlap to the competitor strain suggesting other factors having stronger effects than resource competition. This study provides fundamental insights into how bacterial communities are shaped in heterogeneous environments and a framework to predict competition outcomes.

Response of dissolved organic matter (DOM) and microbial community to submerged macrophytes restoration in lakes: A review

Microorganisms play a crucial role in the biogeochemical processes of Dissolved Organic Matter (DOM), and the properties of DOM also significantly influence changes in microbial community characteristics. This interdependent relationship is vital for the flow of matter and energy within aquatic ecosystems. The presence, growth state, and community characteristics of submerged macrophytes determine the susceptibility of lakes to eutrophication, and restoring a healthy submerged macrophyte community is an effective way to address this issue. However, the transition from eutrophic lakes dominated by planktic algae to medium or low trophic lakes dominated by submerged macrophytes involves significant changes. Changes in aquatic vegetation have greatly affected the source, composition, and bioavailability of DOM. The adsorption and fixation functions of submerged macrophytes determine the migration and storage of DOM and other substances from water to sediment. Submerged macrophytes regulate the characteristics and distribution of microbial communities by controlling the distribution of carbon sources and nutrients in the lake. They further affect the characteristics of the microbial community in the lake environment through their unique epiphytic microorganisms. The unique process of submerged macrophyte recession or restoration can alter the DOM-microbial interaction pattern in lakes through its dual effects on DOM and microbial commu-----nities, ultimately changing the stability of carbon and mineralization pathways in lakes, such as the release of methane and other greenhouse gases. This review provides a fresh perspective on the dynamic changes of DOM and the role of the microbiome in the future of lake ecosystems.

Metabolic interaction models recapitulate leaf microbiota ecology

Resource allocation affects the structure of microbiomes, including those associated with living hosts. Understanding the degree to which this dependency determines interspecies interactions may advance efforts to control host-microbiome relationships. We combined synthetic community experiments with computational models to predict interaction outcomes between plant-associated bacteria. We mapped the metabolic capabilities of 224 leaf isolates from Arabidopsis thaliana by assessing the growth of each strain on 45 environmentally relevant carbon sources in vitro. We used these data to build curated genome-scale metabolic models for all strains, which we combined to simulate >17,500 interactions. The models recapitulated outcomes observed in planta with >89% accuracy, highlighting the role of carbon utilization and the contributions of niche partitioning and cross-feeding in the assembly of leaf microbiomes.

The aeromicrobiome: the selective and dynamic outer-layer of the Earth's microbiome

The atmosphere is an integral component of the Earth's microbiome. Abundance, viability, and diversity of microorganisms circulating in the air are determined by various factors including environmental physical variables and intrinsic and biological properties of microbes, all ranging over large scales. The aeromicrobiome is thus poorly understood and difficult to predict due to the high heterogeneity of the airborne microorganisms and their properties, spatially and temporally. The atmosphere acts as a highly selective dispersion means on large scales for microbial cells, exposing them to a multitude of physical and chemical atmospheric processes. We provide here a brief critical review of the current knowledge and propose future research directions aiming at improving our comprehension of the atmosphere as a biome.

Linking plant functional genes to rhizosphere microbes: a review

The importance of rhizomicrobiome in plant development, nutrition acquisition and stress tolerance is unquestionable. Relevant plant genes corresponding to the above functions also regulate rhizomicrobiome construction. Deciphering the molecular regulatory network of plant-microbe interactions could substantially contribute to improving crop yield and quality. Here, the plant gene-related nutrient uptake, biotic and abiotic stress resistance, which may influence the composition and function of microbial communities, are discussed in this review. In turn, the influence of microbes on the expression of functional plant genes, and thereby plant growth and immunity, is also reviewed. Moreover, we have specifically paid attention to techniques and methods used to link plant functional genes and rhizomicrobiome. Finally, we propose to further explore the molecular mechanisms and signalling pathways of microbe-host gene interactions, which could potentially be used for managing plant health in agricultural systems.

Fungal community remediate quartz tailings soil under plant combined with urban sludge treatments

Introduction

Tailings can cause extensive damage to soil structure and microbial community. Phytoremediation is an effective strategy for remedied tailings soil due to its environmentally friendly and low-cost advantage. Fungi play a crucial role in nutrient cycling, stress resistance, stabilizing soil structure, and promoting plant growth. However, the fungal community variation in phytoremediation remains largely unexplored.

Methods

We analyzed soil fungal community based on high-throughput sequencing during three plant species combined with urban sludge to remediate quartz tailings soil.

Results

The results indicated that the fungal diversity was significantly increased with plant diversity, and the highest fungal diversity was in the three plant species combination treatments. Moreover, the fungal diversity was significantly decreased with the addition of urban sludge compared with plant treatments, while the abundance of potential beneficial fungi such as Cutaneotrichosporon, Apiotrichum, and Alternaria were increased. Notably, the fungal community composition in different plant species combination treatments were significant difference at the genus level. The addition of urban sludge increased pH, available phosphorus (AP), and available nitrogen (AN) content that were the main drivers for fungal community composition. Furthermore, the fungal networks of the plant treatments had more nodes and edges, higher connectedness, and lower modularity than plant combined with urban sludge treatments.

Conclusion

Our results showed that three plant species combined with urban sludge treatments improved fungal community and soil properties. Our results provide insights for quartz tailings soil remediation using plant-fungi- urban sludge.

Resolving metabolic interaction mechanisms in plant microbiomes

Metabolic interactions are fundamental to the assembly and functioning of microbiomes, including those of plants. However, disentangling the molecular basis of these interactions and their specific roles remains a major challenge. Here, we review recent applications of experimental and computational methods toward the elucidation of metabolic interactions in plant-associated microbiomes. We highlight studies that span various scales of taxonomic and environmental complexity, including those that test interaction outcomes in vitro and in planta by deconstructing microbial communities. We also discuss how the continued integration of multiple methods can further reveal the general ecological characteristics of plant microbiomes, as well as provide strategies for applications in areas such as improved plant protection, bioremediation, and sustainable agriculture.

Bacterial community are more susceptible to nanoplastics than algae community in aquatic ecosystems dominated by submerged macrophytes

As a ubiquitous emerging pollutant, microplastics can interact with algal and bacterial communities in aquatic ecosystems. Currently, knowledge on how microplastics influence algae/bacteria is mostly limited to toxicity tests using either monocultures of algae/bacteria or specific algal-bacterial consortium. However, information on the effect of microplastics on algal and bacterial communities in natural habitats is not easily available. Here, we conducted a mesocosm experiment to test the effect of nanoplastics on algal and bacterial communities in aquatic ecosystems dominated by different submerged macrophytes. The community structure of algae and bacteria suspended in the water column (planktonic) and attached to the surface of submerged macrophytes (phyllospheric) were identified, respectively. Results showed that both planktonic and phyllospheric bacteria were more susceptible to nanoplastics, and these variations driven by decreased bacterial diversity and increased abundance of microplastic-degrading taxa, especially in aquatic systems dominated by V. natans. The community composition of both algae and bacteria were influenced to varying degrees by nanoplastics and/or plant types, but RDA results showed that only bacterial community composition was strongly correlated with environmental variables. Correlation network analysis showed that nanoplastics not only reduced the intensity of associations between planktonic algae and bacteria (average degree reduced from 4.88 to 3.24), but also reduced proportion of positive correlations (from 64% to 36%). Besides, nanoplastics also decreased the algal/bacterial connections between planktonic and phyllospheric habitats. Our study elucidates the potential interactions between nanoplastics and algal-bacterial community in natural aquatic ecosystems. These findings suggest that in aquatic ecosystems, bacterial community are more vulnerable to nanoplastics and may serve as a protective barrier for algae community. Further research is needed to reveal the protective mechanism of bacteria against algae at the community level.

The overlooked functions of trichomes: Water absorption and metal detoxication

Trichomes are epidermal outgrowths on plant shoots. Their roles in protecting plants against herbivores and in the biosynthesis of specialized metabolites have long been recognized. Recently, studies are increasingly showing that trichomes also play important roles in water absorption and metal detoxication, with these roles having important implications for ecology, the environment, and agriculture. However, these two functions of trichomes have been largely overlooked and much remains unknown. In this review, we show that the trichomes of 37 plant species belonging to 14 plant families are involved in water absorption, while the trichomes of 33 species from 13 families are capable of sequestering metals within their trichomes. The ability of trichomes to absorb water results from their decreased hydrophobicity compared to the remainder of the leaf surface as well as the presence of special structures for collecting and absorbing water. In contrast, the metal detoxication function of trichomes results not only from the good connection of their basal cells to the underlying vascular tissues, but also from the presence of metal-chelating ligands and transporters within the trichomes themselves. Knowledge gaps and critical future research questions regarding these two trichome functions are highlighted. This review improves our understanding on trichomes.

Above- and below-ground microbiome in the annual developmental cycle of two olive tree varieties

The olive tree is a hallmark crop in the Mediterranean region. Its cultivation is characterized by an enormous variability in existing genotypes and geographical areas. As regards the associated microbial communities of the olive tree, despite progress, we still lack comprehensive knowledge in the description of these key determinants of plant health and productivity. Here, we determined the prokaryotic, fungal and arbuscular mycorrhizal fungal (AMF) microbiome in below- (rhizospheric soil, roots) and above-ground (phyllosphere and carposphere) plant compartments of two olive varieties 'Koroneiki' and 'Chondrolia Chalkidikis' grown in Southern and Northern Greece respectively, in five developmental stages along a full fruit-bearing season. Distinct microbial communities were supported in above- and below-ground plant parts; while the former tended to be similar between the two varieties/locations, the latter were location specific. In both varieties/locations, a seasonally stable root microbiome was observed over time; in contrast the plant microbiome in the other compartments were prone to changes over time, which may be related to seasonal environmental change and/or to plant developmental stage. We noted that olive roots exhibited an AMF-specific filtering effect (not observed for bacteria and general fungi) onto the rhizosphere AMF communities of the two olive varieties/locations/, leading to the assemblage of homogenous intraradical AMF communities. Finally, shared microbiome members between the two olive varieties/locations include bacterial and fungal taxa with putative functional attributes that may contribute to olive tree tolerance to abiotic and biotic stress.

Distinct Phyllosphere Microbiome of Wild Tomato Species in Central Peru upon Dysbiosis

Plants are colonized by myriads of microbes across kingdoms, which affect host development, fitness, and reproduction. Hence, plant microbiomes have been explored across a broad range of host species, including model organisms, crops, and trees under controlled and natural conditions. Tomato is one of the world's most important vegetable crops; however, little is known about the microbiota of wild tomato species. To obtain insights into the tomato microbiota occurring in natural environments, we sampled epiphytic microbes from leaves of four tomato species, Solanum habrochaites, S. corneliomulleri, S. peruvianum, and S. pimpinellifolium, from two geographical locations within the Lima region of Peru over 2 consecutive years. Here, a high-throughput sequencing approach was applied to investigate microbial compositions including bacteria, fungi, and eukaryotes across tomato species and geographical locations. The phyllosphere microbiome composition varies between hosts and location. Yet, we identified persistent microbes across tomato species that form the tomato microbial core community. In addition, we phenotypically defined healthy and dysbiotic samples and performed a downstream analysis to reveal the impact on microbial community structures. To do so, we compared microbial diversities, unique OTUs, relative abundances of core taxa, and microbial hub taxa, as well as co-occurrence network characteristics in healthy and dysbiotic tomato leaves and found that dysbiosis affects the phyllosphere microbial composition in a host species-dependent manner. Yet, overall, the present data suggests an enrichment of plant-promoting microbial taxa in healthy leaves, whereas numerous microbial taxa containing plant pathogens occurred in dysbiotic leaves.Concluding, we identify the core phyllosphere microbiome of wild tomato species, and show that the overall phyllosphere microbiome can be impacted by sampling time point, geographical location, host genotype, and plant health. Future studies in these components will help understand the microbial contribution to plant health in natural systems and can be of use in cultivated tomatoes.

Crop microbiome: their role and advances in molecular and omic techniques for the sustenance of agriculture

This review is an effort to provide in-depth knowledge of microbe's interaction and its role in crop microbiome using combination of advanced molecular and OMICS technology to translate this information for the sustenance of agriculture. Increasing population, climate change and exhaustive agricultural practices either influenced nutrient inputs of soil or generating biological and physico-chemical deterioration of the soils and affecting the agricultural productivity and agro-ecosystems. Alarming concerns toward food security and crop production claim for renewed attention in microbe-based farming practices. Microbes are omnipresent (soil, water, and air) and their close association with plants would help to accomplish sustainable agriculture goals. In the last few decades, the search for beneficial microbes in crop production, soil fertilization, disease management, and plant growth promotion is the thirst for eco-friendly agriculture. The crop microbiome opens new paths to utilize beneficial microbes and manage pathogenic microbes through integrated advanced biotechnology. The crop microbiome helps plants acquire nutrients, growth, resilience against phytopathogens, and tolerance to abiotic stresses, such as heat, drought, and salinity. Despite the emergent functionality of the crop microbiome as a complicated constituent of the plant fitness, our understanding of how the functionality of microbiome influenced by numerous factors including genotype of host, climatic conditions, mobilization of minerals, soil composition, nutrient availability, interaction between nexus of microbes, and interactions with other external microbiomes is partially understood. However, the structure, composition, dynamics, and functional contribution of such cultured and uncultured crop microbiome are least explored. The advanced biotechnological approaches are efficient tools for acquiring the information required to investigate the microbiome and extract data to develop high yield producing and resistant variety crops. This knowledge fills the fundamental gap between the theoretical concepts and the operational use of these advanced tools in crop microbiome studies. Here, we review (1) structure and composition of crop microbiome, (2) microbiome-mediated role associated with crops fitness, (3) Molecular and -omics techniques for exploration of crop microbiome, and (4) current approaches and future prospectives of crop microbiome and its exploitation for sustainable agriculture. Recent -omic approaches are influential tool for mapping, monitoring, modeling, and management of crops microbiome. Identification of crop microbiome, using system biology and rhizho-engineering, can help to develop future bioformulations for disease management, reclamation of stressed agro-ecosystems, and improved productivity of crops. Nano-system approaches combined with triggering molecules of crop microbiome can help in designing of nano-biofertilizers and nano-biopesticides. This combination has numerous merits over the traditional bioinoculants. They stimulate various defense mechanisms in plants facing stress conditions; provide bioavailability of nutrients in the soil, helps mitigate stress conditions; and enhance chances of crops establishment.

Elevated O3 concentrations alter the compartment-specific microbial communities inhabiting rust-infected poplars

Elevated ozone (O₃ ) can affect the susceptivity of plants to rust pathogens. However, the collective role of microbiomes involved in such interaction remains largely elusive. We exposed two cultivated poplar clones exhibiting differential O₃ sensitivities, to non-filtered ambient air (NF), NF + 40 ppb or NF + 60 ppb O₃ -enriched air in field open-top chambers and then inoculated Melampsora larici-populina urediniospores to study their response to rust infection and to investigate how microbiomes inhabiting four compartments (phyllosphere, rhizosphere, root endosphere, bulk soil) are involved in this response. We found that hosts with higher O₃ sensitivity had significantly lower rust severity than hosts with lower sensitivity. Furthermore, the effect of increased O₃ on the diversity and composition of microbial communities was highly dependent on poplar compartments, with the microbial network complexity patterns being completely opposite between the two clones. Notably, microbial source analysis estimated that phyllosphere fungal communities predominately derived from root endosphere and vice versa, suggesting a potential transmission mechanism between plant above- and below-ground systems. These promising results suggest that further investigations are needed to better understand the interactions of abiotic and biotic stresses on plant performance and the role of the microbiome in driving these changes.

Quercus ilex Phyllosphere Microbiome Environmental-Driven Structure and Composition Shifts in a Mediterranean Contex

The intra- and interdomain phyllosphere microbiome features of Quercus ilex L. in a Mediterranean context is reported. We hypothesized that the main driver of the phyllosphere microbiome might be the season and that atmospheric pollutants might have a co-effect. Hence, we investigated the composition of epiphytic bacteria and fungi of leaves sampled in urban and natural areas (in Southern Italy) in summer and winter, using microscopy and metagenomic analysis. To assess possible co-effects on the composition of the phyllosphere microbiome, concentrations of particulate matter and polycyclic aromatic hydrocarbons (PAHs) were determined from sampled leaves. We found that environmental factors had a significative influence on the phyllosphere biodiversity, altering the taxa relative abundances. Ascomycota and Firmicutes were higher in summer and in urban areas, whereas a significant increase in Proteobacteria was observed in the winter season, with higher abundance in natural areas. Network analysis suggested that OTUs belonging to Acidobacteria, Cytophagia, unkn. Firmicutes(p), Actinobacteria are keystone of the Q. ilex phyllosphere microbiome. In addition, 83 genes coding for 5 enzymes involved in PAH degradation pathways were identified. Given that the phyllosphere microbiome can be considered an extension of the ecosystem services offered by trees, our results can be exploited in the framework of Next-Generation Biomonitoring.

Ecology and functional potential of phyllosphere yeasts

The phyllosphere (i.e., the aerial parts of plants) harbors a rich microbial life, including bacteria, fungi, viruses, and yeasts. Current knowledge of yeasts stems primarily from industrial and medical research on Saccharomyces cerevisiae and Candida albicans, both of which can be found on plant tissues. For most other yeasts found in the phyllosphere, little is known about their ecology and functions. Here, we explore the diversity, dynamics, interactions, and genomics of yeasts associated with plant leaves and how tools and approaches developed for model yeasts can be adopted to disentangle the ecology and natural functions of phyllosphere yeasts. A first genomic survey exemplifies that we have only scratched the surface of the largely unexplored functional potential of phyllosphere yeasts.

Fungi are more transient than bacteria in caterpillar gut microbiomes

Despite an increasing number of studies on caterpillar (Insecta: Lepidoptera) gut microbiota, bacteria have been emphasized more than fungi. Therefore, we lack data on whether fungal microbiota is resident or transient and shaped by factors similar to those of bacteria. We sampled nine polyphagous caterpillar species from several tree species at multiple sites to determine the factors shaping leaf and gut bacterial and fungal microbiota as well as the extent to which caterpillars acquire microbiota from their diet. We performed 16S and ITS2 DNA metabarcoding of the leaves and guts to determine the composition and richness of the respective microbiota. While spatial variables shaped the bacterial and fungal microbiota of the leaves, they only affected fungi in the guts, whereas the bacteria were shaped primarily by caterpillar species, with some species harboring more specific bacterial consortia. Leaf and gut microbiota significantly differed; in bacteria, this difference was more pronounced. The quantitative similarity between leaves and guts significantly differed among caterpillar species in bacteria but not fungi, suggesting that some species have more transient bacterial microbiota. Our results suggest the complexity of the factors shaping the gut microbiota, while highlighting interspecific differences in microbiota residency within the same insect functional group.

Community structure and function of epiphytic bacteria attached to three submerged macrophytes

In aquatic ecosystems, large amounts of epiphytic bacteria living on the leaf surfaces of submerged macrophytes play important roles in affecting plant growth and biogeochemical cycling. The restoration of different submerged macrophytes has been considered an effective measure to improve eutrophic lakes. However, the community ecology of epiphytic bacteria is far from well understood for different submerged macrophytes. In this study, we used quantitative PCR, 16S rRNA gene high-throughput sequencing and functional prediction analysis to explore the structure and function of epiphytic bacteria in an aquatic ecosystem recovered by three submerged macrophytes (Hydrilla verticillata, Vallisneria natans and Potamogeton maackianus) during two growth periods. The results showed that the community compositions and functions of epiphytic bacterial communities on the submerged macrophyte hosts were different from those of the planktonic bacterial communities in the surrounding water. The alpha diversity of the epiphytic bacterial community was significantly higher in October than in July, and the community compositions and functions differed significantly in July and October. Among the three submerged macrophytes, the structures and functions of the epiphytic bacterial community exhibited obvious differences, and some specific taxa were enriched on the biofilms of the three plants. The alpha diversity and the abundance of functions related to nitrogen and phosphorus transformation were higher in the epiphytic bacteria of P. maackianus. In summary, these results provide clues for understanding the distribution and formation mechanisms of epiphytic bacteria on submerged macrophyte leaves and their roles in freshwater ecosystems.