Mycorrhizal associations relate to stable convergence in plant-microbial competition for nitrogen absorption under high nitrogen conditions.

Nitrogen (N) immobilization (Nim, including microbial N assimilation) and plant N uptake (PNU) are the two most important pathways of N retention in soils. The ratio of Nim to PNU (hereafter Nim:PNU ratio) generally reflects the degree of N limitation for plant growth in terrestrial ecosystems. However, the key factors driving the pattern of Nim:PNU ratio across global ecosystems remain unclear. Here, using a global data set of 1018 observations from 184 studies, we examined the relative importance of mycorrhizal associations, climate, plant, and soil properties on the Nim:PNU ratio across terrestrial ecosystems. Our results show that mycorrhizal fungi type (arbuscular mycorrhizal (AM) or ectomycorrhizal (EM) fungi) in combination with soil inorganic N mainly explain the global variation in the Nim:PNU ratio in terrestrial ecosystems. In AM fungi-associated ecosystems, the relationship between Nim and PNU displays a weaker negative correlation (r = -.06, p < .001), whereas there is a stronger positive correlation (r = .25, p < .001) in EM fungi-associated ecosystems. Our meta-analysis thus suggests that the AM-associated plants display a weak interaction with soil microorganisms for N absorption, while EM-associated plants cooperate with soil microorganisms. Furthermore, we find that the Nim:PNU ratio for both AM- and EM-associated ecosystems gradually converge around a stable value (13.8 ± 0.5 for AM- and 12.1 ± 1.2 for EM-associated ecosystems) under high soil inorganic N conditions. Our findings highlight the dependence of plant-microbial interaction for N absorption on both plant mycorrhizal association and soil inorganic N, with the stable convergence of the Nim:PNU ratio under high soil N conditions.

Modulation of plant immunity and biotic interactions under phosphate deficiency.

Phosphorus (P) is an essential macronutrient for plant life and growth. P is primarily acquired in the form of inorganic phosphate (Pi) from soil. To cope with Pi deficiency, plants have evolved an elaborate system to improve Pi acquisition and utilization through an array of developmental and physiological changes, termed Pi starvation response (PSR). Plants also assemble and manage mutualistic microbes to enhance Pi uptake, through integrating PSR and immunity signaling. A trade-off between plant growth and defense favors the notion that plants lower a cellular state of immunity to accommodate host-beneficial microbes for nutrition and growth at the cost of infection risk. However, the existing data indicate that plants selectively activate defense responses against pathogens, but do not or less against non-pathogens, even under nutrient deficiency. In this review, we highlight recent advances in the principles and mechanisms with which plants balance immunity and growth-related processes to optimize their adaptation to Pi deficiency.

Time-dependent interaction modification generated from plant-soil feedback.

Pairwise interactions between species can be modified by other community members, leading to emergent dynamics contingent on community composition. Despite the prevalence of such higher-order interactions, little is known about how they are linked to the timing and order of species' arrival. We generate population dynamics from a mechanistic plant-soil feedback model, then apply a general theoretical framework to show that the modification of a pairwise interaction by a third plant depends on its germination phenology. These time-dependent interaction modifications emerge from concurrent changes in plant and microbe populations and are strengthened by higher overlap between plants' associated microbiomes. The interaction between this overlap and the specificity of microbiomes further determines plant coexistence. Our framework is widely applicable to mechanisms in other systems from which similar time-dependent interaction modifications can emerge, highlighting the need to integrate temporal shifts of species interactions to predict the emergent dynamics of natural communities.

Microbiome and floral associations of a wild bee using biodiversity survey collections.

The health of bees can be assessed through their microbiome, which serves as a biomarker indicating the presence of both beneficial and harmful microorganisms within a bee community. This study presents the characterisation of the bacterial, fungal, and plant composition on the cuticle of adult bicoloured sweat bees (Agapostemon virescens). These bees were collected using various methods such as pan traps, blue vane traps and sweep netting across the northern extent of their habitat range. Non-destructive methods were employed to extract DNA from the whole pinned specimens of these wild bees. Metabarcoding of the 16S rRNA, ITS and rbcL regions was then performed. The study found that the method of collection influenced the detection of certain microbial and plant taxa. Among the collection methods, sweep net samples showed the lowest fungal alpha diversity. However, minor differences in bacterial or fungal beta diversity suggest that no single method is significantly superior to others. Therefore, a combination of techniques can cater to a broader spectrum of microbial detection. The study also revealed regional variations in bacterial, fungal and plant diversity. The core microbiome of A. virescens comprises two bacteria, three fungi and a plant association, all of which are commonly detected in other wild bees. These core microbes remained consistent across different collection methods and locations. Further extensive studies of wild bee microbiomes across various species and landscapes will help uncover crucial relationships between pollinator health and their environment.

Recent progress in the role of seed endophytic bacteria as plant growth-promoting microorganisms and biocontrol agents.

The importance of microorganisms residing within the host plant for their growth and health is increasingly acknowledged, yet the significance of microbes associated with seeds, particularly seed endophytic bacteria, remains underestimated. Seeds harbor a wide range of bacteria that can boost the growth and resilience of their host plants against environmental challenges. These endophytic associations also offer advantages for germination and seedling establishment, as seed endophytic bacteria are present during the initial stages of plant growth and development. Furthermore, plants can selectively choose bacteria possessing beneficial traits, which are subsequently transmitted through seeds to confer benefits to future generations. Interestingly, even with the ongoing discovery of endophytes in seeds through high-throughput sequencing methods, certain endophytes remain challenging to isolate and culture from seeds, despite their high abundance. These challenges pose difficulties in studying seed endophytes, making many of their effects on plants unclear. In this article, a framework for understanding the assembly and function of seed endophytes, including their sources and colonization processes was outlined in detail and available research on bacterial endophytes discovered within the seeds of various plant species has also been explored. Thus, this current review aims to provide valuable insights into the mechanism of underlying seed endophytic bacteria-host plant interactions and offers significant recommendations for utilizing the seed endophytic bacteria in sustainable agriculture as plant growth promoters and enhancers of environmental stress tolerance.

Evolutionary history of arbuscular mycorrhizal fungi and genomic signatures of obligate symbiosis.

BACKGROUND: The colonization of land and the diversification of terrestrial plants is intimately linked to the evolutionary history of their symbiotic fungal partners. Extant representatives of these fungal lineages include mutualistic plant symbionts, the arbuscular mycorrhizal (AM) fungi in Glomeromycota and fine root endophytes in Endogonales (Mucoromycota), as well as fungi with saprotrophic, pathogenic and endophytic lifestyles. These fungal groups separate into three monophyletic lineages but their evolutionary relationships remain enigmatic confounding ancestral reconstructions. Their taxonomic ranks are currently fluid. RESULTS: In this study, we recognize these three monophyletic linages as phyla, and use a balanced taxon sampling and broad taxonomic representation for phylogenomic analysis that rejects a hard polytomy and resolves Glomeromycota as sister to a clade composed of Mucoromycota and Mortierellomycota. Low copy numbers of genes associated with plant cell wall degradation could not be assigned to the transition to a plant symbiotic lifestyle but appears to be an ancestral phylogenetic signal. Both plant symbiotic lineages, Glomeromycota and Endogonales, lack numerous thiamine metabolism genes but the lack of fatty acid synthesis genes is specific to AM fungi. Many genes previously thought to be missing specifically in Glomeromycota are either missing in all analyzed phyla, or in some cases, are actually present in some of the analyzed AM fungal lineages, e.g. the high affinity phosphorus transporter Pho89. CONCLUSION: Based on a broad taxon sampling of fungal genomes we present a well-supported phylogeny for AM fungi and their sister lineages. We show that among these lineages, two independent evolutionary transitions to mutualistic plant symbiosis happened in a genomic background profoundly different from that known from the emergence of ectomycorrhizal fungi in Dikarya. These results call for further reevaluation of genomic signatures associated with plant symbiosis.

The coordinated responses of host plants to diverse N-acyl homoserine lactones.

In nature, co-evolution shaped balanced entities of host plants and their associated microorganism. Plants maintain this balance by detecting their associated microorganism and coordinating responses to them. Quorum sensing (QS) is a widespread bacterial cell-to-cell communication mechanism to modulate the collective behavior of bacteria. As a well-characterized QS signal, N-acyl homoserine lactones (AHL) also influence plant fitness. Plants need to coordinate their responses to diverse AHL molecules since they might host bacteria producing various AHL. This opinion paper discusses plants response to a mixture of multiple AHL molecules. The function of various phytohormones and WRKY transcription factors seems to be characteristic for plants' response to multiple AHL. Additionally, the perspectives and possible approaches to facilitate further research and the application of AHL-producing bacteria are discussed.

The CRZ1 transcription factor in plant fungi: regulation mechanism and impact on pathogenesis.

Calcium (Ca2+) is a universal signaling molecule that is tightly regulated, and a fleeting elevation in cytosolic concentration triggers a signal cascade within the cell, which is crucial for several processes such as growth, tolerance to stress conditions, and virulence in fungi. The link between calcium and calcium-dependent gene regulation in cells relies on the transcription factor Calcineurin-Responsive Zinc finger 1 (CRZ1). The direct regulation of approximately 300 genes in different stress pathways makes it a hot topic in host-pathogen interactions. Notably, CRZ1 can modulate several pathways and orchestrate cellular responses to different types of environmental insults such as osmotic stress, oxidative stress, and membrane disruptors. It is our belief that CRZ1 provides the means for tightly modulating and synchronizing several pathways allowing pathogenic fungi to install into the apoplast and eventually penetrate plant cells (i.e., ROS, antimicrobials, and quick pH variation). This review discusses the structure, function, regulation of CRZ1 in fungal physiology and its role in plant pathogen virulence.

A strategy for differential abundance analysis of sparse microbiome data with group-wise structured zeros.

Comparing the abundance of microbial communities between different groups or obtained under different experimental conditions using count sequence data is a challenging task due to various issues such as inflated zero counts, overdispersion, and non-normality. Several methods and procedures based on counts, their transformation and compositionality have been proposed in the literature to detect differentially abundant species in datasets containing hundreds to thousands of microbial species. Despite efforts to address the large numbers of zeros present in microbiome datasets, even after careful data preprocessing, the performance of existing methods is impaired by the presence of inflated zero counts and group-wise structured zeros (i.e. all zero counts in a group). We propose and validate using extensive simulations an approach combining two differential abundance testing methods, namely DESeq2-ZINBWaVE and DESeq2, to address the issues of zero-inflation and group-wise structured zeros, respectively. This combined approach was subsequently successfully applied to two plant microbiome datasets that revealed a number of taxa as interesting candidates for further experimental validation.

Effects of Graphene Oxide on Endophytic Bacteria Population Characteristics in Plants from Soils Contaminated by Polycyclic Aromatic Hydrocarbons.

Environmental pollution stands as one of the significant global challenges we face today. Polycyclic aromatic hydrocarbons (PAHs), a class of stubborn organic pollutants, have long been a focal point of bioremediation research. This study aims to explore the impact and mechanisms of graphene oxide (GO) on the phytoremediation effectiveness of PAHs. The results underscore the significant efficacy of GO in accelerating the degradation of PAHs. Additionally, the introduction of GO altered the diversity and community structure of endophytic bacteria within the roots, particularly those genera with potential for PAH degradation. Through LEfSe analysis and correlation studies, we identified specific symbiotic bacteria, such as Mycobacterium, Microbacterium, Flavobacterium, Sphingomonas, Devosia, Bacillus, and Streptomyces, which coexist and interact under the influence of GO, synergistically degrading PAHs. These bacteria may serve as key biological markers in the PAH degradation process. These findings provide new theoretical and practical foundations for the application of nanomaterials in plant-based remediation of polluted soils and showcase the immense potential of plant-microbe interactions in environmental restoration.

Complete telomere-to-telomere genomes uncover virulence evolution conferred by chromosome fusion in oomycete plant pathogens.

Variations in chromosome number are occasionally observed among oomycetes, a group that includes many plant pathogens, but the emergence of such variations and their effects on genome and virulence evolution remain ambiguous. We generated complete telomere-to-telomere genome assemblies for Phytophthora sojae, Globisporangium ultimum, Pythium oligandrum, and G. spinosum. Reconstructing the karyotype of the most recent common ancestor in Peronosporales revealed that frequent chromosome fusion and fission drove changes in chromosome number. Centromeres enriched with Copia-like transposons may contribute to chromosome fusion and fission events. Chromosome fusion facilitated the emergence of pathogenicity genes and their adaptive evolution. Effectors tended to duplicate in the sub-telomere regions of fused chromosomes, which exhibited evolutionary features distinct to the non-fused chromosomes. By integrating ancestral genomic dynamics and structural predictions, we have identified secreted Ankyrin repeat-containing proteins (ANKs) as a novel class of effectors in P. sojae. Phylogenetic analysis and experiments further revealed that ANK is a specifically expanded effector family in oomycetes. These results revealed chromosome dynamics in oomycete plant pathogens, and provided novel insights into karyotype and effector evolution.

Quorum sensing-related activities of beneficial and pathogenic bacteria have important implications for plant and human health.

Eukaryotic organisms coevolved with microbes from the environment forming holobiotic meta-genomic units. Members of host-associated microbiomes have commensalic, beneficial/symbiotic, or pathogenic phenotypes. More than 100 years ago, Lorenz Hiltner, pioneer of soil microbiology, introduced the term 'Rhizosphere' to characterize the observation that a high density of saprophytic, beneficial, and pathogenic microbes are attracted by root exudates. The balance between these types of microbes decide about the health of the host. Nowadays we know, that for the interaction of microbes with all eukaryotic hosts similar principles and processes of cooperative and competitive functions are in action. Small diffusible molecules like (phyto)hormones, volatiles and quorum sensing signals are examples for mediators of interspecies and cross-kingdom interactions. Quorum sensing of bacteria is mediated by different autoinducible metabolites in a density-dependent manner. In this perspective publication, the role of QS-related activities for the health of hosts will be discussed focussing mostly on N-acyl-homoserine lactones (AHL). It is also considered that in some cases very close phylogenetic relations exist between plant beneficial and opportunistic human pathogenic bacteria. Based on a genome and system-targeted new understanding, sociomicrobiological solutions are possible for the biocontrol of diseases and the health improvement of eukaryotic hosts.

Evolution and adaptation of terrestrial plant-associated Plantibacter species into remote marine environments.

Microbes are thought to be distributed and circulated around the world, but the connection between marine and terrestrial microbiomes remains largely unknown. We use Plantibacter, a representative genus associated with plants, as our research model to investigate the global distribution and adaptation of plant-related bacteria in plant-free environments, particularly in the remote Southern Ocean and the deep Atlantic Ocean. The marine isolates and their plant-associated relatives shared over 98% whole-genome average nucleotide identity (ANI), indicating recent divergence and ongoing speciation from plant-related niches to marine environments. Comparative genomics revealed that the marine strains acquired new genes via horizontal gene transfer from non-Plantibacter species and refined existing genes through positive selection to improve adaptation to new habitats. Meanwhile, marine strains retained the ability to interact with plants, such as modifying root system architecture and promoting germination. Furthermore, Plantibacter species were found to be widely distributed in marine environments, revealing an unrecognized phenomenon that plant-associated microbiomes have colonized the ocean, which could serve as a reservoir for plant growth-promoting microbes. This study demonstrates the presence of an active reservoir of terrestrial plant growth-promoting bacteria in remote marine systems and advances our understanding of the microbial connections between plant-associated and plant-free environments at the genome level.

Soil fungal and bacterial communities reflect differently tundra vegetation state transitions and soil physico-chemical properties.

Strong disturbances may induce ecosystem transitions into new alternative states that sustain through plant-soil interactions, such as the transition of dwarf shrub-dominated into graminoid-dominated vegetation by herbivory in tundra. Little evidence exists on soil microbial communities in alternative states, and along the slow process of ecosystem return into the predisturbance state. We analysed vegetation, soil microbial communities and activities as well as soil physico-chemical properties in historical reindeer enclosures in northernmost Finland in the following plot types: control heaths in the surrounding tundra; graminoid-dominated; 'shifting'; and recovered dwarf shrub-dominated vegetation inside enclosures. Soil fungal communities followed changes in vegetation, whereas bacterial communities were more affected by soil physico-chemical properties. Graminoid plots were characterized by moulds, pathotrophs and dark septate endophytes. Ericoid mycorrhizal and saprotrophic fungi were typical for control and recovered plots. Soil microbial communities inside the enclosures showed historical contingency, as their spatial variation was high in recovered plots despite the vegetation being more homogeneous. Self-maintaining feedback loops between plant functional types, soil microbial communities, and carbon and nutrient mineralization act effectively to stabilize alternative vegetation states, but once predisturbance vegetation reestablishes itself, soil microbial communities and physico-chemical properties return back towards their predisturbance state.

Unveiling Methods to Stimulate Plant Resistance against Pathogens.

Plant diseases caused by pathogens pose significant threats to agricultural productivity and food security worldwide. The traditional approach of relying on chemical pesticides for disease management has proven to be unsustainable, emphasizing the urgent need for sustainable and environmentally friendly alternatives. One promising strategy is to enhance plant resistance against pathogens through various methods. This review aims to unveil and explore effective methods for stimulating plant resistance, transforming vulnerable plants into vigilant defenders against pathogens. We discuss both conventional and innovative approaches, including genetic engineering, induced systemic resistance (ISR), priming, and the use of natural compounds. Furthermore, we analyze the underlying mechanisms involved in these methods, highlighting their potential advantages and limitations. Through an understanding of these methods, scientists and agronomists can develop novel strategies to combat plant diseases effectively while minimizing the environmental impact. Ultimately, this research offers valuable insights into harnessing the plant's innate defense mechanisms and paves the way for sustainable disease management practices in agriculture.

The interplay between the inoculation of plant growth-promoting rhizobacteria and the rhizosphere microbiome and their impact on plant phenotype.

Microbial inoculation stands as a pivotal strategy, fostering symbiotic relationships between beneficial microorganisms and plants, thereby enhancing nutrient uptake, bolstering resilience against environmental stressors, and ultimately promoting healthier and more productive plant growth. However, while the advantageous roles of inoculants are widely acknowledged, the precise and nuanced impacts of inoculation on the intricate interactions of the rhizosphere microbiome remain significantly underexplored. This study explores the impact of bacterial inoculation on soil properties, plant growth, and the rhizosphere microbiome. By employing various bacterial strains and a synthetic community (SynCom) as inoculants in common bean plants, the bacterial and fungal communities in the rhizosphere were assessed through 16 S rRNA and ITS gene sequencing. Concurrently, soil chemical parameters, plant traits, and gene expression were evaluated. The findings revealed that bacterial inoculation generally decreased pH and V%, while increasing H+Al and m% in the rhizosphere. It also decreased gene expression in plants related to detoxification, photosynthesis, and defense mechanisms, while enhancing bacterial diversity in the rhizosphere, potentially benefiting plant health. Specific bacterial strains showed varied impacts on rhizosphere microbiome assembly, predominantly affecting rhizospheric bacteria more than fungi, indirectly influencing soil conditions and plants. Notably, Paenibacillus polymyxa inoculation improved plant nitrogen (by 5.2%) and iron levels (by 28.1%), whereas Bacillus cereus boosted mycorrhization rates (by 70%). Additionally, inoculation led to increased complexity in network interactions within the rhizosphere (∼15%), potentially impacting plant health. Overall, the findings highlight the significant impact of introducing bacteria to the rhizosphere, enhancing nutrient availability, microbial diversity, and fostering beneficial plant-microbe interactions.

The influence of tree genus, phylogeny, and richness on the specificity, rarity, and diversity of ectomycorrhizal fungi.

Partner specificity is a well-documented phenomenon in biotic interactions, yet the factors that determine specificity in plant-fungal associations remain largely unknown. By utilizing composite soil samples, we identified the predictors that drive partner specificity in both plants and fungi, with a particular focus on ectomycorrhizal associations. Fungal guilds exhibited significant differences in overall partner preference and avoidance, richness, and specificity to specific tree genera. The highest level of specificity was observed in root endophytic and ectomycorrhizal associations, while the lowest was found in arbuscular mycorrhizal associations. The majority of ectomycorrhizal fungal species showed a preference for one of their partner trees, primarily at the plant genus level. Specialist ectomycorrhizal fungi were dominant in belowground communities in terms of species richness and relative abundance. Moreover, all tree genera (and occasionally species) demonstrated a preference for certain fungal groups. Partner specificity was not related to the rarity of fungi or plants or environmental conditions, except for soil pH. Depending on the partner tree genus, specific fungi became more prevalent and relatively more abundant with increasing stand age, tree dominance, and soil pH conditions optimal for the partner tree genus. The richness of partner tree species and increased evenness of ectomycorrhizal fungi in multi-host communities enhanced the species richness of ectomycorrhizal fungi. However, it was primarily the partner-generalist fungi that contributed to the high diversity of ectomycorrhizal fungi in mixed forests.

Study on endolichenic fungal assemblage in Parmotrema and Heterodermia lichens of Shivamoga, Karnataka.

BACKGROUND: Lichen is a symbiotic association of algae and fungi, recognized as a self-sustaining ecosystem that constitutes an indeterminant number of bacteria, actinomycetes, fungi, and protozoa. We evaluated the endolichenic fungal assemblage given the dearth of knowledge on endolichenic fungi (ELFs), particularly from part of the Central Western Ghats, Karnataka, and conducted a phylogenetic analysis of xylariaceous fungi, the most diversified group of fungi using ITS and ITS+Tub2 gene set. RESULTS: Out of 17 lichen thalli collected from 5 ecoregions, 42 morphospecies recovered, belong to the class Sordariomycetes, Eurotiomycetes, Dothideomycetes, Leotiomycetes, Saccharomycetes. About 19 and 13 ELF genera have been reported from Parmotrema and Heterodermia thallus. Among the ecoregions EC2 showing highest species diversity (Parmotrema (1-D) = 0.9382, (H) = 2.865, Fisher-α = 8.429, Heterodermia (1-D) = 0.8038, H = 1.894, F-α = 4.57) followed the EC3 and EC1. Xylariales are the predominant colonizer reported from at least one thallus from four ecoregions. The morphotypes ELFX04, ELFX05, ELFX08 and ELFX13 show the highest BLAST similarity (> 99%) with Xylaria psidii, X. feejeensis, X. berteri and Hypoxylon fragiforme respectively. Species delimitation and phylogenetic position reveal the closest relation of Xylariaceous ELFs with plant endophytes. CONCLUSIONS: The observation highlights that the deciduous forest harness a high number of endolichenic fungi, a dominant portion of these fungi are non-sporulating and still exist as cryptic. Overall, 8 ELF species recognized based on phylogenetic analysis, including the two newly reported fungi ELFX03 and ELFX06 which are suspected to be new species based on the present evidence. The study proved, that the lichen being rich source to establish fungal diversity and finding new species. Successful amplification of most phylogenetic markers like RPB2, building of comprehensive taxonomic databases and application of multi-omics data are further needed to understand the complex nature of lichen-fungal symbiosis.

pyPGCF: A Python Software for Phylogenomic Analysis, Species Demarcation, Identification of Core, and Fingerprint Proteins of Bacterial Genomes That Are Important for Plants.

This computational protocol describes how to use pyPGCF, a python software package that runs in the linux environment, in order to analyze bacterial genomes and perform: (i) phylogenomic analysis, (ii) species demarcation, (iii) identification of the core proteins of a bacterial genus and its individual species, (iv) identification of species-specific fingerprint proteins that are found in all strains of a species and, at the same time, are absent from all other species of the genus, (v) functional annotation of the core and fingerprint proteins with eggNOG, and (vi) identification of secondary metabolite biosynthetic gene clusters (smBGCs) with antiSMASH. This software has already been implemented to analyze bacterial genera and species that are important for plants (e.g., Pseudomonas, Bacillus, Streptomyces). In addition, we provide a test dataset and example commands showing how to analyze 165 genomes from 55 species of the genus Bacillus. The main advantages of pyPGCF are that: (i) it uses adjustable orthology cut-offs, (ii) it identifies species-specific fingerprints, and (iii) its computational cost scales linearly with the number of genomes being analyzed. Therefore, pyPGCF is able to deal with a very large number of bacterial genomes, in reasonable timescales, using widely available levels of computing power.