Plant-Microbiome Crosstalk: Dawning from Composition and Assembly of Microbial Community to Improvement of Disease Resilience in Plants

Unraveling the Role of Contaminants Reshaping the Microflora in Zea mays Seeds from Heavy Metal-Contaminated and Pristine Environment

Heavy metal (HM) contaminants are the emerging driving force for reshaping the microflora of plants by eradicating the non-tolerance and non-resistant microbes via their lethal effects. Seeds served as a prime source of ancestral microbial diversity hereditary transfer from generation to generation. However, the problem arises when they got exposed to metal contamination, does metal pollutant disrupt the delicate balance of microbial communities within seeds and lead to shifts in their microflora across generations. In this study, the endophytic community within Zea mays seeds was compared across three distinct regions in Yunnan province, China: a HM-contaminated site Ayika (AK), less-contaminated site Sanduoduo (SD), and a non-contaminated Site Dali (DL). High-throughput sequencing techniques were employed to analyze the microbial communities. A total of 492,177 high-quality reads for bacterial communities and 1,001,229 optimized sequences for fungal communities were obtained. These sequences were assigned to 502 and 239 operational taxonomic units (OTUs) for bacteria and fungi, respectively. A higher diversity was recorded in AK samples than in SD and DL. Microbial community structure analysis showed higher diversity and significant fluctuation in specific taxa abundance in the metal-polluted samples exhibiting higher response of microbial flora to HM. In AK samples, bacterial genera such as Gordonia and Burkholderia-Caballeronia-Paraburkholderia were dominant, while in SD Pseudomonas and Streptomyces were dominant. Among the fungal taxa, Fusarium, Saccharomycopsis, and Lecanicillium were prevalent in HM-contaminated sites. Our finding revealed the influential effect of HM contaminants on reshaping the seed microbiome of the Zea mays, showing both the resilience of certain important microbial taxa as well the shifts in the diversity in the contaminated and pristine conditions. The knowledge will benefit to develop effective soil remediation, reclamation, and crop management techniques, and eventually assisting in the extenuation of metal pollution's adverse effects on plant health and agricultural productivity.

Bacterial consortium amendment effectively reduces Pb/Cd bioavailability in soil and their accumulation in wheat

Microbial remediation can maintain the sustainability of farmlands contaminated with heavy metals (HMs). However, the effects of bacterial consortium on crop growth and potential risks under HM stress, as well as its mechanisms, are still unclear compared with a single microorganism. Here, we investigated the effect of a bacterial consortium consisting of some HMs-resistant bacteria, including Bacillus cereus, Bacillus thuringiensis, and Herbaspirillum huttiense, on plant growth promotion and inhibition of Pb/Cd accumulation within different contaminated soil-wheat systems through pot experiments. The results showed that microbial inoculation alleviated HMs-induced growth inhibition by activating antioxidant enzymes and inhibiting lipid peroxidation, and enhanced plant growth in the bacterial consortium. Compared to a single strain (Bacillus cereus, Bacillus thuringiensis, or Herbaspirillum huttiense), the bacterial consortium was more conducive to improving root development and reducing the content of available HMs in soil (4.5-10.3%) and its transfer to shoot (4.3-8.4%). Moreover, bacterial consortium significantly increased soil enzyme activities and available nutrients, resulting in nearly twice that of a single strain on the effect of soil quality and plant growth. Correlation analysis and least square path analysis showed that the bacterial consortium could significantly reduce the HMs-enrichment/transport from soil to shoot than a single strain by regulating soil available HMs and biochemical properties, as well as the parameters for plant growth. This study emphasizes that bacterial consortium promotes the growth of the crop wheat and reduces the risk of HMs entering human food chain, further providing an effective strategy for the safe production of food crops in contaminated soils.

A host shift as the origin of tomato bacterial canker caused by Clavibacter michiganensis

The Actinomycetota (formerly Actinobacteria) genus Clavibacter includes phytopathogens with devasting effects in several crops. Clavibacter michiganensis, the causal agent of tomato bacterial canker, is the most notorious species of the genus. Yet, its origin and natural reservoirs remain elusive, and its populations show pathogenicity profiles with unpredictable plant disease outcomes. Here, we generate and analyse a decade-long genomic dataset of Clavibacter from wild and commercial tomato cultivars, providing evolutionary insights that directed phenotypic characterization. Our phylogeny situates the last common ancestor of C. michiganensis next to Clavibacter isolates from grasses rather than to the sole strain we could isolate from wild tomatoes. Pathogenicity profiling of C. michiganensis isolates, together with C. phaseoli and C. californiensis as sister taxa and the wild tomato strain, was found to be congruent with the proposed phylogenetic relationships. We then identified gene enrichment after the evolutionary event, leading to the appearance of the C. michiganesis clade, including known pathogenicity factors but also hitherto unnoticed genes with the ability to encode adaptive traits for a pathogenic lifestyle. The holistic perspective provided by our evolutionary analyses hints towards a host shift event as the origin of C. michiganensis as a tomato pathogen and the existence of pathogenic genes that remain to be characterized.

Exploring microbial worlds: a review of whole genome sequencing and its application in characterizing the microbial communities

The classical microbiology techniques have inherent limitations in unraveling the complexity of microbial communities, necessitating the pivotal role of sequencing in studying the diversity of microbial communities. Whole genome sequencing (WGS) enables researchers to uncover the metabolic capabilities of the microbial community, providing valuable insights into the microbiome. Herein, we present an overview of the rapid advancements achieved thus far in the use of WGS in microbiome research. There was an upsurge in publications, particularly in 2021 and 2022 with the United States, China, and India leading the metagenomics research landscape. The Illumina platform has emerged as the widely adopted sequencing technology, whereas a significant focus of metagenomics has been on understanding the relationship between the gut microbiome and human health where distinct bacterial species have been linked to various diseases. Additionally, studies have explored the impact of human activities on microbial communities, including the potential spread of pathogenic bacteria and antimicrobial resistance genes in different ecosystems. Furthermore, WGS is used in investigating the microbiome of various animal species and plant tissues such as the rhizosphere microbiome. Overall, this review reflects the importance of WGS in metagenomics studies and underscores its remarkable power in illuminating the variety and intricacy of the microbiome in different environments.

Microbial community diversity analysis of kiwifruit pollen and identification of potential pathogens

The kiwifruit industry typically uses commercial pollen for artificial pollination. However, during the collection of male flowers and pollen production, pollen can be easily contaminated by pathogenic bacteria that cause diseases such as canker and flower rot. Consequently, it is crucial to understand the structure of the pollen microbial community. This study employed Illumina high-throughput sequencing technology to analyze the fungal and bacterial composition in pollen samples from various regions in Shaanxi Province. Concurrently, potential pathogenic strains were isolated using traditional microbial isolation and cultivation techniques, and their molecular identification was performed through 16S rDNA sequence analysis. A tieback test was conducted on healthy branches to verify the pathogenicity of the strains. The results revealed a rich diversity of fungi and bacteria in kiwifruit pollen. At the phylum level, pollen fungi were mainly distributed in Ascomycota, and bacteria were mainly distributed in Proteobacteria and Firmicutes. The dominant fungal genera were Mycosphaerella, Aspergillus, and Cladosporium; the dominant bacterial genera were Weissella, Pantoea, Enterobacter, and Pseudomonas, respectively. Additionally, both Erwinia persicina and Pseudomonas fluorescens, isolated from pollen, exhibited high pathogenicity toward healthy kiwifruit branches. These findings contribute to a deeper understanding of the microbial diversity in commercial kiwifruit pollen used for mass pollination.

Symphony of survival: Insights into cross-talk mechanisms in plants, bacteria, and fungi for strengthening plant immune responses

Plants coexist with a diverse array of microorganisms, predominantly bacteria and fungi, in both natural and agricultural environments. While some microorganisms positively influence plant development and yield, others can cause harm to the host, leading to significant adverse impacts on the environment and the economy. Plant growth-promoting microorganisms (PGPM), including plant growth-promoting bacteria, arbuscular mycorrhizal fungus (AMF), and rhizobia, have been found to increase plant biomass production by synthesizing hormones, fixing nitrogen, and solubilizing phosphate and potassium. Numerous studies have contributed to unraveling the complex process of plant-microbe interactions in recent decades. In light of the increasing global challenges such as population growth, climate change, and resource scarcity, it has become imperative to explore the potential of plant-bacteria-fungi crosstalk in promoting sustainability. This review aims to bridge existing knowledge gaps, providing a roadmap for future research in this dynamic field by synthesizing current knowledge and identifying emerging trends.

Heat Stress and Plant-Biotic Interactions: Advances and Perspectives

Climate change presents numerous challenges for agriculture, including frequent events of plant abiotic stresses such as elevated temperatures that lead to heat stress (HS). As the primary driving factor of climate change, HS threatens global food security and biodiversity. In recent years, HS events have negatively impacted plant physiology, reducing plant's ability to maintain disease resistance and resulting in lower crop yields. Plants must adapt their priorities toward defense mechanisms to tolerate stress in challenging environments. Furthermore, selective breeding and long-term domestication for higher yields have made crop varieties vulnerable to multiple stressors, making them more susceptible to frequent HS events. Studies on climate change predict that concurrent HS and biotic stresses will become more frequent and severe in the future, potentially occurring simultaneously or sequentially. While most studies have focused on singular stress effects on plant systems to examine how plants respond to specific stresses, the simultaneous occurrence of HS and biotic stresses pose a growing threat to agricultural productivity. Few studies have explored the interactions between HS and plant-biotic interactions. Here, we aim to shed light on the physiological and molecular effects of HS and biotic factor interactions (bacteria, fungi, oomycetes, nematodes, insect pests, pollinators, weedy species, and parasitic plants), as well as their combined impact on crop growth and yields. We also examine recent advances in designing and developing various strategies to address multi-stress scenarios related to HS and biotic factors.

Modulation of rhizosphere microbial community and metabolites by bio-functionalized nanoscale silicon oxide alleviates cadmium-induced phytotoxicity in bayberry plants

Cadmium (Cd) is an extremely toxic heavy metal that can originate from industrial activities and accumulate in agricultural soils. This study investigates the potential of biologically synthesized silicon oxide nanoparticles (Bio-SiNPs) in alleviating Cd toxicity in bayberry plants. Bio-SiNPs were synthesized using the bacterial strain Chryseobacterium sp. RTN3 and thoroughly characterized using advanced techniques. A pot experiment results demonstrated that Cd stress substantially reduced leaves biomass, photosynthesis efficiency, antioxidant enzyme activity, and induced oxidative damage in bayberry (Myrica rubra) plants. However, Bio-SiNPs application at 200 mg kg-1 significantly enhanced plant biomass, chlorophyll content (26.4 %), net photosynthetic rate (8.6 %), antioxidant enzyme levels, and mitigated reactive oxygen species production under Cd stress. Bio-SiNPs modulated key stress-related phytohormones by increasing salicylic acid (13.2 %) and abscisic acid (13.7 %) contents in plants. Bio-SiNPs augmented Si deposition on root surfaces, preserving normal ultrastructure in leaf cells. Additionally, 16S rRNA gene sequencing demonstrated that Bio-SiNPs treatment favorably reshaped structure and abundance of specific bacterial groups (Proteobacteria, Actinobacteriota, and Acidobacteriota) in the rhizosphere. Notably, Bio-SiNPs application significantly modulated the key metabolites (phenylacetaldehyde, glycitein, maslinic acid and methylmalonic acid) under both normal and Cd stress conditions. Overall, this study highlights that bio-nanoremediation using Bio-SiNPs enhances tolerance to Cd stress in bayberry plants by beneficially modulating biochemical, microbial, and metabolic attributes.

Bio-formulated chitosan nanoparticles enhance disease resistance against rice blast by physiomorphic, transcriptional, and microbiome modulation of rice (Oryza sativa L.)

Rice blast disease (RBD) caused by Magnaporthe oryzae, threaten food security by cutting agricultural output. Nano agrochemicals are now perceived as sustainable, cost-effective alternatives to traditional pesticides. This study investigated bioformulation of moringa chitosan nanoparticles (M-CsNPs) and their mechanisms for suppressing RBD while minimizing toxic effects on the microenvironment. M-CsNPs, sized 46 nm with semi-spherical morphology, significantly suppressed pathogen growth, integrity, and colonization at 200 mg L-1in vitro. Greenhouse tests with foliar exposure to the same concentration resulted in a substantial 77.7 % reduction in RBD, enhancing antioxidant enzyme activity and plant health. Furthermore, M-CsNPs improved photosynthesis, gas exchange, and the nutritional profile of diseased rice plants. RNA-seq analysis highlighted upregulated defense-related genes in treated rice plants. Metagenomic study showcased reshaping of the rice microbiome, reducing Magnaporthe abundance by 93.5 %. Both healthy and diseased rice plants showed increased microbial diversity, particularly favoring specific beneficial species Thiobacillus, Nitrospira, Nocardioides, and Sphingomicrobium in the rhizosphere and Azonexus, Agarivorans, and Bradyrhizobium in the phyllosphere. This comprehensive study unravels the diverse mechanisms by which M-CsNPs interact with plants and pathogens, curbing M. oryzae damage, promoting plant growth, and modulating the rice microbiome. It underscores the significant potential for effective plant disease management.

The Populations of Two Differently Medicine-Used Plants of Hedyotis diffusa and Hedyotis corymbosa Shoot-Assembling Rich Bacterial and Fungal Communities with Varied Compositions but Conserved Structures

The plant-colonized microbial communities have closely micro-ecological effects on host plant growth and health. There are many medicinal plants in the genus Hedyotis, but it is yet unclear about the shoot-assembled bacterial and fungal communities (SBFC) of Hedyotis plants. Hence, eight plant populations of Hedyotis diffusa (HD) and H. corymbosa (HC) were evaluated with 16S rRNA gene and ITS sequences, for comparing the types, abundance, or/and potential functions of SBFC at plant species- and population levels. In tested HD- and HC-SBFC, 682 fungal operational taxonomic units and 1,329 bacterial zero-radius operational taxonomic units were identified, with rich species compositions and varied alpha diversities. Notably, the SBFC compositions of HD and HC plant populations were exhibited with partly different types and abundances at phylum and genus levels but without significantly different beta diversities at plant species and population levels. Typically, the SBFC of HD and HC plant populations were presented with abundance-different biomarkers, such as Frankiaceae and Bryobacteraceae, and with similar micro-ecological functions of microbial metabolisms of lipids, terpenoids,and xenobiotics. Taken together, HD- and HC-SBFC possessed with varied rich compositions, conservative taxonomic structures, and similar metabolic functions, but with small-scale type and abundance differences at plant species- and population- levels.

Microbial dysbiosis in roots and rhizosphere of grapevines experiencing decline is associated with active metabolic functions

When grapevine decline, characterized by a premature decrease in vigor and yield and sometimes plant death, cannot be explained by pathological or physiological diseases, one may inquire whether the microbiological status of the soil is responsible. Previous studies have shown that the composition and structure of bacterial and fungal microbial communities in inter-row soil are affected in areas displaying vine decline, compared to areas with non-declining vines within the same plot. A more comprehensive analysis was conducted in one such plot. Although soil chemical parameters could not directly explain these differences, the declining vines presented lower vigor, yield, berry quality, and petiole mineral content than those in non-declining vines. The bacterial and fungal microbiome of the root endosphere, rhizosphere, and different horizons of the bulk soil were explored through enzymatic, metabolic diversity, and metabarcoding analysis in both areas. Despite the lower microbial diversity and richness in symptomatic roots and soil, higher microbial activity and enrichment of potentially both beneficial bacteria and pathogenic fungi were found in the declining area. Path modeling analysis linked the root microbial activity to berry quality, suggesting a determinant role of root microbiome in the berry mineral content. Furthermore, certain fungal and bacterial taxa were correlated with predicted metabolic pathways and metabolic processes assessed with Eco-Plates. These results unexpectedly revealed active microbial profiles in the belowground compartments associated with stressed vines, highlighting the interest of exploring the functional microbiota of plants, and more specifically roots and rhizosphere, under stressed conditions.

Ralstonia solanacearum differentially modulates soil physicochemical properties and rhizospheric bacteriome of resistant and susceptible tobacco cultivars

Ralstonia solanacearum is a devastating soilborne pathogen which poses significant yield and economic losses to tobacco production globally. The impact of R. solanacearum on rhizosphere bacteriome and soil physicochemical characteristics in resistant and susceptible tobacco cultivars is poorly understood. This study aims to determine the effect of R. solanacearum on soil physicochemical parameters and rhizosphere bacteriome of resistant (K326) and susceptible (Hongda) tobacco cultivars at various growth stages. Results demonstrated that the contents of available potassium and phosphorus, as well as soil pH were significantly increased in K326 soils (CK and T2) compared with Hongda (T1) after 21, 42, and 63 days post-inoculation (dpi) of R. solanacearum except for available nitrogen which showed an opposite trend. The qPCR results showed a significant decrease in R. solanacearum population in rhizosphere of K326 (T2) compared to the Hongda (T1) at 21 and 63 dpi than that after 42 dpi. The rhizosphere bacteriome analysis through 16S rRNA amplicon sequencing revealed that rhizosphere bacterial community composition was significantly different between two tobacco cultivars (Hongda and K326) and this effect was more prominent after 63 dpi (93 days after post-transplantation), suggesting that each cultivar recruits a unique set of bacterial communities. There was no obvious difference observed in the rhizosphere bacteriome of CK (K326) and T2 (K326), which might be attributed to the same genetic makeup and inherent resistance of K326 to bacterial wilt infection. Analysis of co-occurrence networks revealed that the microbial network in T1 (Hongda) was more complex than those in T2 (K326) and CK (K326), while the networks in CK and T2 were almost identical. The present research highlights the time-course relationship between environmental factors and rhizosphere bacteriome of tobacco cultivars showing different levels of resistance against R. solanacearum. Conclusively, studying the plant-soil-microbe interaction system in susceptible and resistant tobacco cultivars may enable us to develop effective integrated disease control plans for the healthy production of tobacco crops.

The endophytic fungal community plays a crucial role in the resistance of host plants to necrotic bacterial pathogens

Konjac species (Amorphophallus spp.) are the only plant species in the world that are rich in a large amount of konjac glucomannan (KGM). These plants are widely cultivated as cash crops in tropical and subtropical countries in Asia, including China. Pectobacterium carotovorum subsp. carotovorum (Pcc) is one of the most destructive bacterial pathogens of konjac. Here, we analyzed the interactions between Pcc and susceptible and resistant konjac species from multiple perspectives. At the transcriptional and metabolic levels, the susceptible species A. konjac and resistant species A. muelleri exhibit similar molecular responses, activating plant hormone signaling pathways and metabolizing defense compounds such as phenylpropanoids and flavonoids to resist infection. Interestingly, we found that Pcc stress can lead to rapid recombination of endophytic microbial communities within a very short period (96 h). Under conditions of bacterial pathogen infection, the relative abundance of most bacterial communities in konjac tissue decreased sharply compared with that in healthy plants, while the relative abundance of some beneficial fungal communities increased significantly. The relative abundance of Cladosporium increased significantly in both kinds of infected konjac compared to that in healthy plants, and the relative abundance in resistant A. muelleri plants was greater than that in susceptible A. konjac plants. Among the isolated cultivable microorganisms, all three strains of Cladosporium strongly inhibited Pcc growth. Our results further elucidate the potential mechanism underlying konjac resistance to Pcc infection, highlighting the important role of endophytic microbial communities in resisting bacterial pathogen infections, especially the more direct role of fungal communities in inhibiting pathogen growth.

Effects of fungal endophytes and arbuscular mycorrhizal fungi on growth of Echium vulgare and alkannin/shikonin and their derivatives production in roots

Endophytic fungi as well as arbuscular mycorrhizal fungi (AMF) are known to stimulate plant growth and production of secondary metabolites in medicinal plants. Here, 10 endophytic fungi isolated from roots of wild Alkanna tinctoria plants and 5 AMF purchased from the Glomeromycota in vitro collection were evaluated, during two successive three-month greenhouse experiments, on the growth of Echium vulgare and alkannin/shikonin and their derivatives (A/Sd) production in the roots. Some of the endophytic fungi tested significantly increased plant growth parameters as compared to the control: Cladosporium allicinum, Cadophora sp., Clonostachys sp., Trichoderma hispanicum and Leptosphaeria ladina increased root volume, Plectosphaerella sp. And T. hispanicum root fresh weight and root water retention and T. hispanicum plant water retention. However, none of these fungi impacted A/Sd production. Conversely, none of the AMF strains tested impacted plant growth parameters, but those inoculated with Rhizophagus intraradices MUCL 49410 had a significantly higher concentration of alkannin/shikonin (A/S), acetyl-A/S, β,β- dimethylacryl-A/S, isovaleryl-A/S and total A/Sd, compared to the control plants. Further studies are needed to investigate the mechanisms involved in the production of A/Sd in plants associated to specific endophytic fungi/AMF and on the cultivation conditions required for optimal production of these compounds.

From concept to reality: Transforming agriculture through innovative rhizosphere engineering for plant health and productivity

The plant rhizosphere is regarded as a microbial hotspot due to a wide array of root exudates. These root exudates comprise diverse organic compounds such as phenolic, polysaccharides, flavonoids, fatty acids, and amino acids that showed chemotactic responses towards microbial communities and mediate significant roles in root colonization. The rhizospheric microbiome is a crucial driver of plant growth and productivity, contributing directly or indirectly by facilitating nutrient acquisition, phytohormone modulation, and phosphate solubilization under normal and stressful conditions. Moreover, these microbial candidates protect plants from pathogen invasion by secreting antimicrobial and volatile organic compounds. To enhance plant fitness and yield, rhizospheric microbes are frequently employed as microbial inoculants. However, recent developments have shifted towards targeted rhizosphere engineering or microbial recruitments as a practical approach to constructing desired plant rhizospheres for specific outcomes. The rhizosphere, composed of plants, microbes, and soil, can be modified in several ways to improve inoculant efficiency. Rhizosphere engineering is achieved through three essential mechanisms: a) plant-mediated modifications involving genetic engineering, transgenics, and gene editing of plants; b) microbe-mediated modifications involving genetic alterations of microbes through upstream or downstream methodologies; and c) soil amendments. These mechanisms shape the rhizospheric microbiome, making plants more productive and resilient under different stress conditions. This review paper comprehensively summarizes the various aspects of rhizosphere engineering and their potential applications in maintaining plant health and achieving optimum agricultural productivity.

Genetic architecture of the response of Arabidopsis thaliana to a native plant-growth-promoting bacterial strain

By improving plant nutrition and alleviating abiotic and biotic stresses, plant growth-promoting bacteria (PGPB) can help to develop eco-friendly and sustainable agricultural practices. Besides climatic conditions, soil conditions, and microbe-microbe interactions, the host genotype influences the effectiveness of PGPB. Yet, most GWAS conducted to characterize the genetic architecture of response to PGPB are based on non-native interactions between a host plant and PGPB strains isolated from the belowground compartment of other plants. In this study, a GWAS was set up under in vitro conditions to describe the genetic architecture of the response of Arabidopsis thaliana to the PGPB Pseudomonas siliginis, by inoculating seeds of 162 natural accessions from the southwest of France with one strain isolated from the leaf compartment in the same geographical region. Strong genetic variation of plant growth response to this native PGPB was observed at a regional scale, with the strain having a positive effect on the vegetative growth of small plants and a negative effect on the vegetative growth of large plants. The polygenic genetic architecture underlying this negative trade-off showed suggestive signatures of local adaptation. The main eco-evolutionary relevant candidate genes are involved in seed and root development.

Dynamic interplay between nano-enabled agrochemicals and the plant-associated microbiome

The plant-associated microbiome is known to be a critical component for crop growth, nutrient acquisition, resistance to pathogens, and abiotic stress tolerance. Conventional approaches have been attempted to manipulate the plant-soil microbiome to improve plant performance; however, several issues have arisen, such as collateral negative impacts on microbiota composition. The lack of reliability and robustness of conventional techniques warrants efforts to develop novel alternative strategies. Nano-enabled approaches have emerged as promising platforms for enhancing agricultural sustainability and global food security. Specifically, the use of engineered nanomaterials (ENMs) as nanoscale agrochemicals has great potential to modulate the plant-associated microbiome. We review the dynamic interplay between nano-agrochemicals and the plant-associated microbiome for the safe development and use of nano-enabled microbiome engineering.

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.

Description of Xanthocytophaga agilis sp. nov. and Xanthocytophaga flavus sp. nov. of the new genus Xanthocytophaga gen. nov and the proposal of Rhodocytophagaceae fam. nov. within the order Cytophagales

Four Gram-staining-negative, aerobic, yellow-pigmented and rod-shaped bacteria, named strains BD1B2-1T, NT2B1T, YF14B1 and DM2B3-1, were isolated from four rhizosphere soil samples of banana in China. Comparison of the 16S rRNA gene sequences showed that all these strains were most closely related to an invalidly published species, 'Rhodocytophaga rosea' 172606-1, with similarities ranging from 87.7 to 88.0%. According to the phylogenomic analysis, the four strains were clustered in an independent lineage and closely related to the genus Rhodocytophaga. The genomic sizes of these strains were approximately 9.49-9.77 Mbp with the DNA G + C contents of 38.8-39.0 mol%. They all contained C16:1 ω5c, iso-C15:0 and iso-C17:0 3-OH as the major fatty acids and menaquinone 7 as the only respiratory quinone. They all had phosphatidylethanolamine as the major polar lipids. Based on phenotypic and phylogenomic characteristics, the four strains should represent two novel species within a novel genus, for which the names Xanthocytophaga agilis gen. nov., sp. nov. (BD1B2-1T = GDMCC 1.2890T = JCM 35374T) and Xanthocytophaga flavus sp. nov. (NT2B1T = GDMCC 1.2889T = JCM 35375T) are proposed; the former is assigned as the type species of the novel genus Xanthocytophaga gen. nov. In addition, based on the phenotypic and phylogenomic data, we proposed to reclassify the existing genus Rhodocytophaga in the family Cytophagaceae into a novel family Rhodocytophagaceae fam. nov. The novel family consists of the type genus Rhodocytophaga and the novel genus Xanthocytophaga.

Pathogen Profile of Klebsiella variicola, the Causative Agent of Banana Sheath Rot

Banana (Musa spp.) is an important fruit and food crop worldwide. In recent years, banana sheath rot has become a major problem in banana cultivation, causing plant death and substantial economic losses. Nevertheless, the pathogen profile of this disease has not been fully characterized. Klebsiella variicola is a versatile bacterium capable of colonizing different hosts, such as plants, humans, insects, and animals, and is recognized as an emerging pathogen in various hosts. In this study, we obtained 12 bacterial isolates from 12 different banana samples showing banana sheath rot in Guangdong and Guangxi Provinces, China. Phylogenetic analysis based on 16S rRNA sequences confirmed that all 12 isolates were K. variicola strains. We sequenced the genomes of these strains, performed comparative genomic analysis with other sequenced K. variicola strains, and found a lack of consistency in accessory gene content among these K. variicola strains. However, prediction based on the pan-genome of K. variicola revealed 22 unique virulence factors carried by the 12 pathogenic K. variicola isolates. Microbiome and microbial interaction network analysis of endophytes between the healthy tissues of diseased plants and healthy plants of two cultivars showed that Methanobacterium negatively interacts with Klebsiella in banana plants and that Herbaspirillum might indirectly inhibit Methanobacterium to promote Klebsiella growth. These results suggest that banana sheath rot is caused by the imbalance of plant endophytes and opportunistic pathogenic bacteria, providing an important basis for research and control of this disease.[Formula: see text] Copyright © 2023 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license.

Diversity Analysis and Function Prediction of Bacterial Communities in the Different Colored Pericarp of Citrus reticulata cv. 'Shatangju' Due to 'Candidatus Liberibacter asiaticus' Infection

Huanglongbing (HLB), caused by the Candidatus Liberibacter spp., is the most devastating disease in the citrus industry. HLB significantly affects and alters the microbial community structure or potential function of the microbial community of leaves and roots. However, it is unknown how the microbial community structure of the pericarp with different pigments is affected by Candidatus Liberibacter asiaticus (CLas). This study identified the enriched taxa of the microbial community in the citrus pericarp with normal or abnormal pigment and determine the effects of HLB on the pericarp microbial community using 16S rRNA-seq. The alpha and beta diversity and composition of microbial communities were significantly different between normal and abnormal pigment pericarp tissues of ripe fruits infected by CLas. Firmicutes, Actinobacteriota, Bacteroidota, Acidobacteriota, and Desulfobacterota dominated the pericarp microbiota composition in WDYFs (whole dark yellow fruits) samples. The relative abundance of most genera in WDYFs was higher than 1%, such as Burkholderia, and Pelomonas. However, with the exception of the HLB pathogen, the relative abundance of most genera in the abnormal-colored pericarp samples was less than 1%. CLas decreased the relative abundance of pericarp taxonomic. The predicted function of microbial was more plentiful and functional properties in the WDYF sample, such as translation, ribosomal structure and biogenesis, amino acid transport and metabolism, energy production and conversion, and some other clusters of orthologous groups (COG) except for cell motility. The results of this study offer novel insights into understanding the composition of microbial communities of the CLas-affected citrus pericarps and contribute to the development of biological control strategies for citrus against Huanglongbing.

The Influence of Cone Age and Urbanisation on the Diversity and Community Composition of Culturable Seed Fungal Endophytes within Native Australian Banksia ericifolia L.f. subsp. ericifolia

Seed fungal endophytes play a crucial role in assisting the overall health and success of their host plant; however, little is known about the factors that influence the diversity and composition of these endophytes, particularly with respect to how they change over time and within urban environments. Using culturing techniques, morphological analyses, and Sanger sequencing, we identified the culturable seed fungal endophytes of Banksia ericifolia at two urban and two natural sites in Sydney, New South Wales, Australia. A total of 27 Operational Taxonomic Units were obtained from 1200 seeds. Older cones were found to contain, on average, more colonised endophytes than younger cones. Species richness was also significantly influenced by cone age, with older cones being more speciose. Between urban and natural sites, the overall community composition did not change, although species richness and diversity were greatest at urban sites. Understanding how these endophytes vary in time and space may help provide an insight into the transmission pathways used and the potential role they play within the development and survival of the seed. This knowledge may also be crucial for restoration purposes, especially regarding the need to consider endophyte viability in ex situ seed collection and storage in seed-banking practices.

The Microbial Connection to Sustainable Agriculture

Microorganisms are an important element in modeling sustainable agriculture. Their role in soil fertility and health is crucial in maintaining plants' growth, development, and yield. Further, microorganisms impact agriculture negatively through disease and emerging diseases. Deciphering the extensive functionality and structural diversity within the plant-soil microbiome is necessary to effectively deploy these organisms in sustainable agriculture. Although both the plant and soil microbiome have been studied over the decades, the efficiency of translating the laboratory and greenhouse findings to the field is largely dependent on the ability of the inoculants or beneficial microorganisms to colonize the soil and maintain stability in the ecosystem. Further, the plant and its environment are two variables that influence the plant and soil microbiome's diversity and structure. Thus, in recent years, researchers have looked into microbiome engineering that would enable them to modify the microbial communities in order to increase the efficiency and effectiveness of the inoculants. The engineering of environments is believed to support resistance to biotic and abiotic stressors, plant fitness, and productivity. Population characterization is crucial in microbiome manipulation, as well as in the identification of potential biofertilizers and biocontrol agents. Next-generation sequencing approaches that identify both culturable and non-culturable microbes associated with the soil and plant microbiome have expanded our knowledge in this area. Additionally, genome editing and multidisciplinary omics methods have provided scientists with a framework to engineer dependable and sustainable microbial communities that support high yield, disease resistance, nutrient cycling, and management of stressors. In this review, we present an overview of the role of beneficial microbes in sustainable agriculture, microbiome engineering, translation of this technology to the field, and the main approaches used by laboratories worldwide to study the plant-soil microbiome. These initiatives are important to the advancement of green technologies in agriculture.

Biofilm-Forming Ability of Phytopathogenic Bacteria: A Review of its Involvement in Plant Stress

Phytopathogenic bacteria not only affect crop yield and quality but also the environment. Understanding the mechanisms involved in their survival is essential to develop new strategies to control plant disease. One such mechanism is the formation of biofilms; i.e., microbial communities within a three-dimensional structure that offers adaptive advantages, such as protection against unfavorable environmental conditions. Biofilm-producing phytopathogenic bacteria are difficult to manage. They colonize the intercellular spaces and the vascular system of the host plants and cause a wide range of symptoms such as necrosis, wilting, leaf spots, blight, soft rot, and hyperplasia. This review summarizes up-to-date information about saline and drought stress in plants (abiotic stress) and then goes on to focus on the biotic stress produced by biofilm-forming phytopathogenic bacteria, which are responsible for serious disease in many crops. Their characteristics, pathogenesis, virulence factors, systems of cellular communication, and the molecules implicated in the regulation of these processes are all covered.

Wild Rosa Endophyte M7SB41-Mediated Host Plant's Powdery Mildew Resistance

Our previous studies indicated that endophyte M7SB41 (Seimatosporium sp.) can significantly enhance host plants powdery mildew (PM) resistance. To recover the mechanisms, differentially expressed genes (DEGs) were compared between E+ (endophte-inoculated) and E- (endophyte-free) plants by transcriptomics. A total of 4094, 1200 and 2319 DEGs between E+ and E- were identified at 0, 24, and 72 h after plants had been infected with PM pathogen Golovinomyces cichoracearum, respectively. Gene expression pattern analysis displayed a considerable difference and temporality in response to PM stress between the two groups. Transcriptional profiling analysis revealed that M7SB41 induced plant resistance to PM through Ca²⁺ signaling, salicylic acid (SA) signaling, and the phenylpropanoid biosynthesis pathway. In particular, we investigated the role and the timing of the SA and jasmonic acid (JA)-regulated defensive pathways. Both transcriptomes and pot experiments showed that SA-signaling may play a prominent role in PM resistance conferred by M7SB41. Additionally, the colonization of M7SB41 could effectively increase the activities and the expression of defense-related enzymes under PM pathogen stress. Meanwhile, our study revealed reliable candidate genes from TGA (TGACG motif-binding factor), WRKY, and pathogenesis-related genes related to M7SB41-mediate resistance. These findings offer a novel insight into the mechanisms of endophytes in activating plant defense responses.

Reconnoitering the capabilities of nodule endophytic Pantoea dispersa for improved nodulation and grain yield of chickpea (Cicer arietinum L.)

Microorganisms belonging to root and soil provide a wide range of services and benefits to the plant by promoting plant growth and controlling phytopathogens. This study aimed to isolate endophytic bacteria from the root nodules of chickpea (Cicer arietinum L.) and determine their potential in improving plant growth. A total of nineteen different bacterial morphotypes were isolated from root nodules of chickpea and characterized in vitro for plant growth promotion abilities. All bacterial isolates were able to produce indole acetic acid at varying levels, out of which MCA19 was screened as the most efficient indole acetic acid producer (10.25 µg mL^-1). MCA8, MCA9, MCA10, MCA11, MCA16, MCA17 and MCA19 were positive for phosphate solubilization, out of which MCA9 was best phosphate solubilizer (18.8 µg mL^-1). All bacterial strains showed varying ability to grow on nitrogen-free media. Hydrogen cyanide, pectinase, and cellulase production ability were also observed in isolates, in which MCA9, MCA12, MCA17 and MCA19 were found best. Based on in vitro testing, five isolates MCA2, MCA9, MCA11, MCA17 and MCA19 were selected for further studies. Bacterial isolates MCA9, MCA11, MCA17 and MCA19 were identified by 16S rRNA gene sequence analysis as Pantoea dispersa while MCA2 as Rhizobium pusense. This is the first report on the existence of Pantoea dispersa in the root nodules of chickpea. In pot experiment, a maximum increase of 30% was recorded in plant dry weight upon the application of MCA19. Under field conditions, bacterial isolates, MCA2, MCA11 and MCA19 significantly enhanced nodulation and yield parameters of chickpea, compared to control. Pantoea dispersa MCA19 displayed the highest plant growth-promoting potential by increasing 38% grain yield. Our results indicate that Pantoea dispersa MCA19 is a promising biofertilizer for future applications.

Evaluating the hologenome concept by analyzing the root-endosphere microbiota of chimeric plants

The hologenome concept considers the entity formed by a host and its microbiota, the holobiont, as new level of hierarchical organization subject to neutral and selective forces. We used grafted plants to formally evaluate the hologenome concept. We analyzed the root-endosphere microbiota of two independent watermelon and grapevine plant systems, including ungrafted and reciprocal-grafting combinations. Grafted and ungrafted hosts harbor markedly different microbiota compositions. Furthermore, the results indicate a non-random assembly of bacterial communities inhabiting the root endosphere of chimeric plants with interactive effect of both the rootstock and scion on the recruitment of microorganisms. Because chimeric plants did not have a random microbiota, the null hypothesis that holobionts assemble randomly and hologenome concept is an intellectual construction only can be rejected. The study supports the relevance of hologenome as biological level of organization and opens new avenues for a better fundamental understanding of plants as holobionts.

Bio-Functionalized Manganese Nanoparticles Suppress Fusarium Wilt in Watermelon (Citrullus lanatus L.) by Infection Disruption, Host Defense Response Potentiation, and Soil Microbial Community Modulation

The use of nanofabricated materials is being explored for the potential in crop disease management. Chemically synthesized micronutrient nanoparticles (NPs) have been shown to reduce crop diseases; however, the potential of biogenic manganese NPs (bio-MnNPs) in disease control is unknown. Here, the potential and mechanism of bio-MnNPs in suppression of watermelon Fusarium wilt, caused by Fusarium oxysporum f. sp. niveum (Fon) are reported. Bio-MnNPs are synthesized by cell-free cultural filtrate of a waterrmelon rhizosphere bacterial strain Bacillus megaterium NOM14, and are found spherical in shape with a size range of 27.0-65.7 nm. Application of bio-MnNPs at 100 µg mL^-1 increases Mn content in watermelon roots/shoots and improves growth performance through enhancing multiple physiological processes, including antioxidative capacity. Bio-MnNPs at 100 µg mL^-1 suppress Fusarium wilt through inhibiting colonization and invasive growth of Fon in watermelon roots/stems, and inhibit Fon vegetative growth, conidiation, conidial morphology, and cellular integrity. Bio-MnNPs potentiate watermelon systemic acquired resistance by triggering the salicylic acid signaling upon Fon infection, and reshape the soil microbial community by improving fungal diversity. These findings demonstrate that bio-MnNPs suppress watermelon Fusarium wilt by multiple ex planta and in planta mechanisms, and offer a promising nano-enabled strategy for the sustainable management of crop diseases.

Nitrogen Fertilizer Application Alters the Root Endophyte Bacterial Microbiome in Maize Plants, but Not in the Stem or Rhizosphere Soil

Plant-associated microorganisms that affect plant development, their composition, and their functionality are determined by the host, soil conditions, and agricultural practices. How agricultural practices affect the rhizosphere microbiome has been well studied, but less is known about how they might affect plant endophytes. In this study, the metagenomic DNA from the rhizosphere and endophyte communities of root and stem of maize plants was extracted and sequenced with the "diversity arrays technology sequencing," while the bacterial community and functionality (organized by subsystems from general to specific functions) were investigated in crops cultivated with or without tillage and with or without N fertilizer application. Tillage had a small significant effect on the bacterial community in the rhizosphere, but N fertilizer had a highly significant effect on the roots, but not on the rhizosphere or stem. The relative abundance of many bacterial species was significantly different in the roots and stem of fertilized maize plants, but not in the unfertilized ones. The abundance of N cycle genes was affected by N fertilization application, most accentuated in the roots. How these changes in bacterial composition and N genes composition might affect plant development or crop yields has still to be unraveled. IMPORTANCE We investigated the bacterial community structure in the rhizosphere, root, and stem of maize plants cultivated under different agricultural techniques, i.e., with or without N fertilization, and with or without tillage. We found that the bacterial community was defined mostly by the plant compartment and less by agricultural techniques. In the roots, N fertilizer application affected the bacterial community structure, the microbiome functionality, and the abundance of genes involved in the N cycle, but the effect in the rhizosphere and stem was much smaller. Contrary, tillage did not affect the maize microbiome. This study enriches our knowledge about the plant-microbiome system and how N fertilization application affected it.

Changes in Microbial Community Structure in Response to Gummosis in Peach Tree Bark

Peach gummosis disease has been identified as a serious challenge in Korean agriculture and has developed to become a major cause of agricultural productivity losses. However, treatments for gummosis have not been systemically established and studies of the microbiome closely related to this plant disease are lacking. Therefore, we analyzed the bacterial and fungal communities in the bark and rhizosphere soil of healthy peach trees and those with gummosis. Through high-throughput sequencing, we obtained unprecedented insights into the bacterial and fungal dynamics of each group, including their diversity and taxonomic classification, as well as network analyses. We found that the presence of gummosis drives a significantly higher alpha diversity in the bark bacterial community. Peach gummosis bark mycobiomes included greater numbers of opportunistic pathogens such as Ascochyta, Botryosphaeria, Saccharomyces, Nectriaceae_NA, Trametes, and Valsaceae_NA. However, the microbiome also included bacteria beneficial to plant growth and the production of polysaccharides-namely, 1174-901-12, Catenibacterium, Cutibacterium, Friedmanniella, Methylobacterium-Methylorubrum, Pseudomonas, Rhodobacter, and Sphingomonas. Furthermore, we confirmed that gummosis induced a more complex structure in the bark microbiome network. We conclude that the findings of this study provide a valuable aid in profiling the overall peach tree microbial ecosystem, which can be utilized to develop precise biomarkers for the early diagnosis of gummosis.

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

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

The functional microbiota of on- and off-year moso bamboo (Phyllostachys edulis) influences the development of the bamboo pest Pantana phyllostachysae

BACKGROUND

Development of Pantana phyllostachysae, a moso bamboo pest, is affected by its diet. Understanding the mechanism underlying the different insect-resistant capacities of on- and off-year moso bamboo fed by P. phyllostachysae is crucial for managing pest outbreaks. As microbes were proven to influence plant immunity, we compared gut microbial communities of P. phyllostachysae with different diets by metabarcoding sequencing. By using sterilization assay, microbes were removed from leaf surfaces, and thus we confirmed that microbes inhabiting moso bamboo leaves impact the weight of P. phyllostachysae larva. Furthermore, the gut microbial communities of P. phyllostachysae fed on on- and off-year bamboo leaves were compared, to identify the functional microbial communities that impact the interaction between bamboo leaves and P. phyllostachysae.

RESULTS

We found that species from orders Lactobacillales and Rickettsiales are most effective within functional microbiota. Functional prediction revealed that gut microbes of larva fed on on-year leaves were related to naphthalene degradation, while those fed on off-year leaves were related to biosynthesis of ansamycins, polyketide sugar unit biosynthesis, metabolism of xenobiotics, and tetracycline biosynthesis. Most functional microbes are beneficial to the development of larva that feed on on-year bamboo leaves, but damage the balance of intestinal microenvironment and immune systems of those larva that feed on off-year leaves.

CONCLUSIONS

This work developed an efficient strategy for microbiome research of Lepidopteran insects and provided insights into microbiota related to the interaction between host plants and P. phyllostachysae. We provided microbial candidates for the ecological control of P. phyllostachysae according to the function of effective microbiota.

Bacillus licheniformis JF-22 to Control Meloidogyne incognita and Its Effect on Tomato Rhizosphere Microbial Community

Meloidogyne incognita is one of the most destructive soil pests, causing serious economic losses in tomato production. Here, in vitro experiments demonstrated that the Bacillus licheniformis strain JF-22 has the potential to prevent M. incognita infection. A pot experiment confirmed that B. licheniformis strain JF-22 isolated from the tomato rhizosphere soil and planted in the tomato root-knot nematode disease area effectively prevented and controlled M. incognita, reducing its negative effect on tomato growth. Additionally, the composition of volatile substances secreted by B. licheniformis strain JF-22 was analyzed using solid-phase microextraction and gas chromatography–mass spectrometry. We detected acetoin, 2,3-Butanediol, [R-(R*,R*) ]-, and hexamethyl cyclotrisiloxane as the main components among these volatiles. Using MiSeq sequencing technology and bioinformatics, we analyzed the influence of B. licheniformis strain JF-22 on the microbial community of the tomato rhizosphere. B. licheniformis strain JF-22 changed the composition of the microbial community; particularly, it significantly reduced the diversity of the fungal community. Furthermore, using the FUNGuild and PICRUSt databases, we predicted the effect of JF-22 on microbial community function. In conclusion, B. licheniformis strain JF-22 may be considered as a potential biocontrol agent against M. incognita.

Metagenomic Analyses of the Soybean Root Mycobiome and Microbiome Reveal Signatures of the Healthy and Diseased Plants Affected by Taproot Decline

Invading pathogens interact with plant-associated microbial communities, which can be altered under the pressure of pathogen infection. Limited information exists on plant-microbe interactions occurring during natural outbreaks in agricultural fields. Taproot decline (TRD) of soybean is an emerging disease caused by Xylaria necrophora. TRD disease occurrence and yield loss associated with TRD are outstanding issues in soybean production. We applied nuclear ribosomal DNA Internal Transcribed Spacers and 16S rRNA gene taxonomic marker sequencing to define the composition of the fungal and bacterial communities associated with healthy and diseased soybean roots collected from the Mississippi Delta. The plant compartment was a significant factor regulating taxonomic diversity, followed by the disease status of the plant. TRD impacted the root endophytes, causing imbalances; at the intermediate and advanced stages of TRD, X. necrophora decreased mycobiome diversity, whereas it increased microbiome richness. Networks of significant co-occurrence and co-exclusion relationships revealed direct and indirect associations among taxa and identified hubs with potential roles in assembling healthy and TRD-affected soybean biomes. These studies advance the understanding of host-microbe interactions in TRD and the part of biomes in plant health and disease.

Crops Change the Morphology, Abundance, and Mass of Microplastics in Mollisols of Northeast China

Degradation of microplastics (MPs) by both physicochemical and biological processes in the natural environment is determined by the enzymes inside the soil, and which was severely influenced by crop growth and straw amendment (SA). However, it is still unclear how crop growth and SA influence degradation of MPs in soils. In this study, both catalase and sucrase were measured, and the stereomicroscope combined with microscopic infrared spectroscopy and scanning electron microscope (SEM) was used to detect the morphology and quantity of low-density polyethylene microplastic (LDPE-MP) and low-density polypropylene microplastic (LDPP-MP), after crop growth (maize and soybean, with and without SA, 1 and 2% MP) in an outdoor pot experiment, in the Mollisols. The results showed that the growth of the crops changed the morphology, functional groups (e.g., methylene, carbonyl), total mass, and abundance ratio of MPs of different sizes. These were possibly caused by enzymes that were significantly influenced by crop types, abundance, and types of MPs in the soils. Maize growth decreased the mass of LDPE-MP and LDPP-MP by 28.7 and 32.7%, respectively, and 2% (w/w) of LDPP-MP addition in soil decreased mass of 9%, which was higher than that in 1% (w/w) LDPP-MP addition in soil. Soybean growth with SA decreased the mass of LDPE-MP and LDPP-MP by 36.6 and 20.7%, respectively, than the control treatment (CK). Compared with CK, both crop growth and SA changed the abundance of MPs of different sizes and decreased the mean size of MPs. The LDPE-MP could be more easily degraded by enzymes in the soils compared to LDPP-MP when the MP size was smaller with surface roughness. Generally, both maize and soybean growth can accelerate MP change in soils, and MP change process was mainly determined by SA, MP types, and the dose effect of MP.

Multi-Omics of Pine Wood Nematode Pathogenicity Associated With Culturable Associated Microbiota Through an Artificial Assembly Approach

Pinewood nematode (PWN), the causal agent of pine wilt disease (PWD), causes massive global losses of Pinus species each year. Bacteria and fungi existing in symbiosis with PWN are closely linked with the pathogenesis of PWD, but the relationship between PWN pathogenicity and the associated microbiota is still ambiguous. This study explored the relationship between microbes and the pathogenicity of PWN by establishing a PWN-associated microbe library, and used this library to generate five artificial PWN-microbe symbiont (APMS) assemblies with gnotobiotic PWNs. The fungal and bacterial communities of different APMSs (the microbiome) were explored by next-generation sequencing. Furthermore, different APMSs were used to inoculate the same Masson pine (Pinus massoniana) cultivar, and multi-omics (metabolome, phenomics, and transcriptome) data were obtained to represent the pathogenicity of different APMSs at 14 days post-inoculation (dpi). Significant positive correlations were observed between microbiome and transcriptome or metabolome data, but microbiome data were negatively correlated with the reactive oxygen species (ROS) level in the host. Five response genes, four fungal genera, four bacterial genera, and nineteen induced metabolites were positively correlated with the ROS level, while seven induced metabolites were negatively correlated. To further explore the function of PWN-associated microbes, single genera of functional microbes (Mb1-Mb8) were reloaded onto gnotobiotic PWNs and used to inoculate pine tree seedlings. Three of the genera (Cladophialophora, Ochroconis, and Flavobacterium) decreased the ROS level of the host pine trees, while only one genus (Penicillium) significantly increased the ROS level of the host pine tree seedlings. These results demonstrate a clear relationship between associated microbes and the pathogenicity of PWN, and expand the knowledge on the interaction between PWD-induced forest decline and the PWN-associated microbiome.

Effect of the Nanoparticle Exposures on the Tomato Bacterial Wilt Disease Control by Modulating the Rhizosphere Bacterial Community

Ralstonia Solanacearum is one of the most infectious soil-borne bacterial plant pathogens, causing tomato bacterial wilt (TBW). Nanotechnology is an emerging area of research, particularly the application of nanoparticles (NPs) as nanopesticides to manage plant disease is gaining attention nowadays. However, the interaction between NPs and rhizosphere bacterial communities remains largely elusive. This study indicated that metal NPs (CuO, ZnO, and FeO) reduced the incidence of bacterial wilt to varying degrees and affected the composition and structure of the rhizosphere bacterial community. The results revealed that the application of metal oxide NPs can improve the morphological and physiological parameters of TBW infected tomato plants. Among all, CuONPs amendments significantly increase the Chao1 and Shannon index. In the early stage (the second week), it significantly reduces the relative abundance of pathogens. However, the relative abundance of beneficial Streptomyces bacteria increased significantly, negatively correlated with the relative abundance of pathogenic bacteria. In addition, the nano-treatment group will enrich some potential beneficial bacteria such as species from Sphingomonadaceae, Rhizobiaceae, etc. In general, our research provides evidence and strategies for preventing and controlling soil-borne disease tomato bacterial wilt with metal oxide NPs.

Plant-Microbe Interaction: Aboveground to Belowground, from the Good to the Bad

Soil health and fertility issues are constantly addressed in the agricultural industry. Through the continuous and prolonged use of chemical heavy agricultural systems, most agricultural lands have been impacted, resulting in plateaued or reduced productivity. As such, to invigorate the agricultural industry, we would have to resort to alternative practices that will restore soil health and fertility. Therefore, in recent decades, studies have been directed towards taking a Magellan voyage of the soil rhizosphere region, to identify the diversity, density, and microbial population structure of the soil, and predict possible ways to restore soil health. Microbes that inhabit this region possess niche functions, such as the stimulation or promotion of plant growth, disease suppression, management of toxicity, and the cycling and utilization of nutrients. Therefore, studies should be conducted to identify microbes or groups of organisms that have assigned niche functions. Based on the above, this article reviews the aboveground and below-ground microbiomes, their roles in plant immunity, physiological functions, and challenges and tools available in studying these organisms. The information collected over the years may contribute toward future applications, and in designing sustainable agriculture.