Search

Background: The symbiosis between arbuscular mycorrhizal fungi (AMF) and plants often stimulates plant growth, increases agricultural yield, reduces costs, thereby providing significant economic benefits. AMF can also benefit plants through affecting the rhizosphere microbial community, but the underlying mechanisms remain unclear. Using Rhizophagus intraradices as a model AMF species, we assessed how AMF influences the bacterial composition and functional diversity through 16 S rRNA gene sequencing and non-targeted metabolomics analysis in the rhizosphere of aluminum-sensitive soybean that were inoculated with pathogenic fungus Nigrospora oryzae and phosphorus-solubilizing fungus Talaromyces verruculosus in an acidic soil. Results: The inoculation of R. intraradices, N. oryzae and T. verruculosus didn't have a significant influence on the levels of soil C, N, and P, or various plant characteristics such as seed weight, crude fat and protein content. However, their inoculation affected the structure, function and nutrient dynamics of the resident bacterial community. The co-inoculation of T. verruculosus and R. intraradices increased the relative abundance of Pseudomonas psychrotolerans, which was capable of N-fixing and was related to cry-for-help theory (plants signal for beneficial microbes when under stress), within the rhizosphere. R. intraradices increased the expression of metabolic pathways associated with the synthesis of unsaturated fatty acids, which was known to enhance plant resistance under adverse environmental conditions. The inoculation of N. oryzae stimulated the stress response inside the soil environment by enriching the polyene macrolide antifungal antibiotic-producing bacterial genus Streptomyces in the root endosphere and upregulating two antibacterial activity metabolic pathways associated with steroid biosynthesis pathways in the rhizosphere. Although inoculation of pathogenic fungus N. oryzae enriched Bradyrhizobium and increased soil urease activity, it had no significant effects on biomass and N content of soybean. Lastly, the host niches exhibited differences in the composition of the bacterial community, with most N-fixing bacteria accumulating in the endosphere and Rhizobium vallis only detected in the endosphere. Conclusions: Our findings demonstrate that intricate interactions between AMF, associated core fungi, and the soybean root-associated ecological niches co-mediate the regulation of soybean growth, the dynamics of rhizosphere soil nutrients, and the composition, function, and metabolisms of the root-associated microbiome in an acidic soil. Highlights: AMF R. intraradices improved soybean stress resistance by recruiting specific PGPR and upregulating plant resistance promotion metabolic pathway. The pathogenic fungus N. oryzae stimulated the stress response by enriching the antifungal antibiotic production bacteria and upregulating the antibacterial reaction-associated metabolic pathways. The utility evaluation of some microbial agents on host plants should consider their potential impact on Olsen-P content in acidic soils with limited P availability. The sampling compartments (i.e., host niches of the soybean rhizosphere) exerted greater influence on the assembly and shift of the bacterial community than the application of microbial agents. [ABSTRACT FROM AUTHOR]

Abstract Background The symbiosis between arbuscular mycorrhizal fungi (AMF) and plants often stimulates plant growth, increases agricultural yield, reduces costs, thereby providing significant economic benefits. AMF can also benefit plants through affecting the rhizosphere microbial community, but the underlying mechanisms remain unclear. Using Rhizophagus intraradices as a model AMF species, we assessed how AMF influences the bacterial composition and functional diversity through 16 S rRNA gene sequencing and non-targeted metabolomics analysis in the rhizosphere of aluminum-sensitive soybean that were inoculated with pathogenic fungus Nigrospora oryzae and phosphorus-solubilizing fungus Talaromyces verruculosus in an acidic soil. Results The inoculation of R. intraradices, N. oryzae and T. verruculosus didn’t have a significant influence on the levels of soil C, N, and P, or various plant characteristics such as seed weight, crude fat and protein content. However, their inoculation affected the structure, function and nutrient dynamics of the resident bacterial community. The co-inoculation of T. verruculosus and R. intraradices increased the relative abundance of Pseudomonas psychrotolerans, which was capable of N-fixing and was related to cry-for-help theory (plants signal for beneficial microbes when under stress), within the rhizosphere. R. intraradices increased the expression of metabolic pathways associated with the synthesis of unsaturated fatty acids, which was known to enhance plant resistance under adverse environmental conditions. The inoculation of N. oryzae stimulated the stress response inside the soil environment by enriching the polyene macrolide antifungal antibiotic-producing bacterial genus Streptomyces in the root endosphere and upregulating two antibacterial activity metabolic pathways associated with steroid biosynthesis pathways in the rhizosphere. Although inoculation of pathogenic fungus N. oryzae enriched Bradyrhizobium and increased soil urease activity, it had no significant effects on biomass and N content of soybean. Lastly, the host niches exhibited differences in the composition of the bacterial community, with most N-fixing bacteria accumulating in the endosphere and Rhizobium vallis only detected in the endosphere. Conclusions Our findings demonstrate that intricate interactions between AMF, associated core fungi, and the soybean root-associated ecological niches co-mediate the regulation of soybean growth, the dynamics of rhizosphere soil nutrients, and the composition, function, and metabolisms of the root-associated microbiome in an acidic soil.

Abstract Hyperaccumulating plants are able to (hyper)accumulate high concentrations of metal(loid)s in their above-ground tissues without any signs of toxicity. Studies on the root-associated microbiome have been previously conducted in relation to hyperaccumulators, yet much remains unknown about the interactions between hyperaccumulating hosts and their microbiomes, as well as the dynamics within these microbial communities. Here, we assess the impact of the plant host on shaping microbial communities of three naturally occurring populations of Noccaea species in Slovenia: Noccaea praecox and co-occurring N. caerulescens from the non-metalliferous site and N. praecox from the metalliferous site. We investigated the effect of metal enrichment on microbial communities and explored the interactions within microbial groups and their environment. The abundance of bacterial phyla was more homogeneous than fungal classes across all three Noccaea populations and across the three root-associated compartments (roots, rhizosphere, and bulk soil). While most fungal and bacterial Operational Taxonomic Units (OTUs) were found at both sites, the metalliferous site comprised more unique OTUs in the root and rhizosphere compartments than the non-metalliferous site. In contrast to fungi, bacteria exhibited differentially significant abundance between the metalliferous and non-metalliferous sites as well as statistically significant correlations with most of the soil parameters. Results revealed N. caerulescens had the highest number of negative correlations between the bacterial phyla, whereas the population from the metalliferous site had the fewest. This decrease was accompanied by a big perturbation in the bacterial community at the metalliferous site, indicating increased selection between the bacterial taxa and the formation of potentially less stable rhizobiomes. These findings provide fundamentals for future research on the dynamics between hyperaccumulators and their associated microbiome.

Plant roots and rhizosphere soils assemble diverse microbial communities, and these root-associated microbiomes profoundly influence host development. Modern wheat has given rise to numerous cultivars for its wide range of ecological adaptations and commercial uses. Variations in nitrogen uptake by different wheat cultivars are widely observed in production practices. However, little is known about the composition and structure of the root-associated microbiota in different wheat cultivars, and it is not sure whether root-associated microbial communities are relevant in host nitrogen absorption. Therefore, there is an urgent need for systematic assessment of root-associated microbial communities and their association with host nitrogen absorption in field-grown wheat. Here, we investigated the root-associated microbial community composition, structure, and keystone taxa in wheat cultivars with different nitrogen absorption characteristics at different stages and their relationships with edaphic variables and host nitrogen uptake. Our results indicated that cultivar nitrogen absorption characteristics strongly interacted with bacterial and archaeal communities in the roots and edaphic physicochemical factors. The impact of host cultivar identity, developmental stage, and spatial niche on bacterial and archaeal community structure and network complexity increased progressively from rhizosphere soils to roots. The root microbial community had a significant direct effect on plant nitrogen absorption, while plant nitrogen absorption and soil temperature also significantly influenced root microbial community structure. The cultivar with higher nitrogen absorption at the jointing stage tended to cooperate with root microbial community to facilitate their own nitrogen absorption. Our work provides important information for further wheat microbiome manipulation to influence host nitrogen absorption. Key points: • Wheat cultivar and developmental stage affected microbiome structure and network. • The root microbial community strongly interacted with plant nitrogen absorption. • High nitrogen absorption cultivar tended to cooperate with root microbiome. [ABSTRACT FROM AUTHOR]

Canola (Brassica napus) is an important broadacre crop, produced under high nitrogen (N) fertilizer application. Modern canola varieties are developed under high N rates but the impacts on root-associated microbiomes of different varieties are unknown. We studied eight canola varieties spanning historical Canadian spring canola development at two sites under high and low N fertility and characterized bacterial and fungal microbiomes in the root and rhizosphere using amplicon sequencing. Environmental conditions and the resulting canola varietal responses strongly affected the root-associated bacterial and fungal microbiomes. Microbes regulated by N fertility in each canola variety were mainly Gammaproteobacteria, Bacteroidia, Actinobacteria, Sordariomycetes, Dothideomycetes, and Agaricomycetes classes. Differentially abundant (DA) microbial taxa showed that N more strongly enriched bacteria in the roots and fungi in the rhizosphere. Each variety had its specific pattern of DA amplicon sequence variants (ASVs) responding to soil N availability, and the profile of DA-ASVs in paired canola varieties were also altered by soil N availability, especially bacteria in the rhizosphere. The yield was strongly associated with a subset of microbial taxa, mainly from Proteobacteria, Actinobacteriota, and Ascomycota. These variety-dependent responses to N and links to yield performance make the root-associated microbiome a promising target for improving the agronomic performance of canola by manipulating microorganisms tailored to soil fertility and plant genotype.

Root-microbiome interactions are of central importance for plant performance and yield. A distinctive feature of legumes is that they engage in symbiosis with N2-fixing rhizobia. If and how the rhizobial symbiotic capacity modulates root-associated microbiomes are still not yet well understood. We determined root-associated microbiomes of soybean inoculated with wild type (WT) or a noeI mutant of Bradyrhizobium diazoefficiens USDA 110 by amplicon sequencing. UPLC-MS/MS was used to analyze root exudates. The noeI gene is responsible for fucose-methylation of Nod factor secreted by USDA 110 WT strain. Soybean roots inoculated with the noeI mutant showed a significant decrease in nodulation and root-flavonoid exudation compared to roots inoculated with WT strain. The noeI mutant-inoculated roots exhibited strong changes in microbiome assembly in the rhizosphere and rhizoplane, including reduced diversity, changed co-occurrence interactions and a substantial depletion of root microbes. Root exudates and soil physiochemical properties were significantly correlated with microbial community shift in the rhizosphere between different rhizobial treatments. These results illustrate that rhizobial symbiotic capacity dramatically alters root-associated microbiomes, in which root exudation and edaphic patterns play a vital role. This study has important implications for understanding the evolution of plant-microbiome interactions.

Dodders (Cuscuta chinensis) are rootless and holoparasitic herbs that can infect a variety of host plants, including the vitally important economic and bioenergy crop soybean (Glycine max). Although dodder parasitism severely affects the physiology of host plants, little is known about its effects on fungal communities and root secondary metabolites in hosts. In this study, variations in root-associated fungal communities and root metabolites of soybean under different parasitism conditions were investigated using ITS rRNA gene sequencing and UPLC–MS/MS metabolome detection technologies. The results showed that dodder parasitism significantly altered the composition and diversity of the fungal communities in the rhizosphere and endosphere of soybean. The relative abundance of the potential pathogenic fungus Alternaria significantly increased in the root endosphere of dodder-parasitized soybean. Furthermore, correlation analysis indicated that the fungal community in the root endosphere was susceptible to soil factors under dodder parasitism. Meanwhile, the content of soil total nitrogen was significantly and positively correlated with the relative abundance of Alternaria in the rhizosphere and endosphere of soybean. Metabolomic analysis indicated that dodder parasitism altered the accumulation of flavonoids in soybean roots, with significant upregulation of the contents of kaempferol and its downstream derivatives under different parasitism conditions. Taken together, this study highlighted the important role of dodder parasitism in shaping the fungal communities and secondary metabolites associated with soybean roots, providing new insights into the mechanisms of multiple interactions among dodder, soybean, microbial communities and the soil environment. [ABSTRACT FROM AUTHOR]

Harnessing the rhizobia-legume symbiosis is a promising strategy to confront sustainability in agriculture. Agricultural research on legume nodulation has mostly focused on abiotic parameters, yet the importance of biotic variables on legumes nodulation is still ambiguous. We explored the variation of bacterial communities in peanut rhizosphere soil under different agricultural practices (peanut fallow rotation and Vicia villosa Roth-peanut rotation) using Illumina sequencing. Samples were collected in 2020 from a 9-year study (2012–2020) located at Dongxiang countryside (Jiangxi province, China). Compared with peanut fallow rotation (PFR), Vicia villosa Roth-peanut rotation (VPR) significantly (p< 0.05) decreased soil pH (by 0.4–3.9%) and number of peanut nodules (by 20–63.7%). By using the Random forest tool, we found that the difference in peanut nodulation was associated with specific microbiome alterations. The indicator taxa positively responded to the peanut nodulation was enriched in the PFR practice, while VPR led to increased abundance of indicator taxa which negatively responded to peanut nodulation. The path analysis indicated that soil pH has an indirect effect on peanut nodulation through its link with the abundance of indicator taxa. Our work provides evidence that the variation in peanut rhizosphere microbial communities was associated with peanut nodulation. [ABSTRACT FROM AUTHOR]

ABSTRACT Plant root-associated microbiomes play critical roles in promoting plant health, productivity, and tolerance to biotic/abiotic stresses. Blueberry (Vaccinium spp.) is adapted to acidic soils, while the interactions of the root-associated microbiomes in this specific habitat under various root microenvironments remain elusive. Here, we investigated the diversity and community composition of bacterial and fungal communities in various blueberry root niches (bulk soil, rhizosphere soil, and root endosphere). The results showed that blueberry root niches significantly affected root-associated microbiome diversity and community composition compared to those of the three host cultivars. Deterministic processes gradually increased along the soil-rhizosphere-root continuum in both bacterial and fungal communities. The co-occurrence network topological features showed that both bacterial and fungal community complexity and intensive interactions decreased along the soil-rhizosphere-root continuum. Different compartment niches clearly influenced bacterial-fungal interkingdom interactions, which were significantly higher in the rhizosphere, and positive interactions gradually dominated the co-occurrence networks from the bulk soil to the endosphere. The functional predictions showed that rhizosphere bacterial and fungal communities may have higher cellulolysis and saprotrophy capacities, respectively. Collectively, the root niches not only affected microbial diversity and community composition but also enhanced the positive interkingdom interactions between bacterial and fungal communities along the soil-rhizosphere-root continuum. This provides an essential basis for manipulating synthetic microbial communities for sustainable agriculture. IMPORTANCE The blueberry root-associated microbiome plays an essential role in its adaptation to acidic soils and in limiting the uptake of soil nutrients by its poor root system. Studies on the interactions of the root-associated microbiome in the various root niches may deepen our understanding of the beneficial effects in this particular habitat. Our study extended the research on the diversity and composition of microbial communities in different blueberry root compartment niches. Root niches dominated the root-associated microbiome compared to that of the host cultivar, and deterministic processes increased from the bulk soil to the endosphere. In addition, bacterial-fungal interkingdom interactions were significantly higher in the rhizosphere, and those positive interactions progressively dominated the co-occurrence network along the soil-rhizosphere-root continuum. Collectively, root niches dominantly affected the root-associated microbiome and the positive interkingdom interactions increased, potentially providing benefits for the blueberry.

ABSTRACT Root-associated microbiomes are essential for the ecological function of the root system. However, their assembly mechanisms in wetland are poorly understood. In this study, we explored and compared the ecological processes of bacterial and fungal communities in water, bulk soil, rhizosphere soil, and root endosphere niches for 3 developmental stages of Typha orientalis at different wetland sites, and assessed the potential functions of root endosphere microbiomes with function prediction. Our findings suggest that the microbial diversity, composition, and interaction networks along the water-soil-plant continuum are shaped predominantly by compartment niche and developmental stage, rather than by wetland site. Source tracking analysis indicated that T. orientalis’ root endosphere is derived primarily from the rhizosphere soil (bacteria 39.9%, fungi 27.3%) and water (bacteria 18.9%, fungi 19.1%) niches. In addition, we found that the assembly of bacterial communities is driven primarily by deterministic processes and fungal communities by stochastic processes. The interaction network among microbes varies at different developmental stages of T. orientalis, and is accompanied by changes in microbial keystone taxa. The functional prediction data supports the distribution pattern of the bacterial and fungal microbiomes, which have different ecological roles at different plant developmental stages, where more beneficial bacterial taxa are observed in the root endosphere in the early stages, but more saprophytic fungi in the late stages. Our findings provide empirical evidence for the assembly, sources, interactions, and potential functions of wetland plant root microbial communities and have significant implications for the future applications of plant microbiomes in the wetland ecosystem. IMPORTANCE Our findings provide empirical evidence for the assembly, sources, interactions, and potential functions of wetland plant root microbial communities, and have significant implications for the future applications of plant microbiomes in the wetland ecosystem.

Objective: To better understand the wetland restoration, the physicochemical property and microbial community in rhizosphere and bulk soil of the living and death Tamarix chinensis covered soil zones were studied. Results: There were differences between growth conditions in the levels of soil pH, salinity, SOM, and nutrient. The living status of T. chinensis exhibited higher capacity of decreasing saline-alkali soil than the death condition of plants, and the living T. chinensis showed higher uptake of N, P, and K as compared with the death samples. Proteobacteria, Bacteroidota, and Chloroflexi were the predominant bacterial communities as revealed via high-throughput sequencing. Conclusions: It is great potential for using halophytes such as T. chinensis to ecological restore the coastal saline-alkali soil. This study could contribute to a better understanding of halophyte growth during the coastal phytoremediation process, and guide theoretically for management of T. chinensis population. [ABSTRACT FROM AUTHOR]

Dodders (Cuscuta chinensis) are rootless and holoparasitic herbs that can infect a variety of host plants, including the vitally important economic and bioenergy crop soybean (Glycine max). Although dodder parasitism severely affects the physiology of host plants, little is known about its effects on fungal communities and root secondary metabolites in hosts. In this study, variations in root-associated fungal communities and root metabolites of soybean under different parasitism conditions were investigated using ITS rRNA gene sequencing and UPLC–MS/MS metabolome detection technologies. The results showed that dodder parasitism significantly altered the composition and diversity of the fungal communities in the rhizosphere and endosphere of soybean. The relative abundance of the potential pathogenic fungus Alternaria significantly increased in the root endosphere of dodder-parasitized soybean. Furthermore, correlation analysis indicated that the fungal community in the root endosphere was susceptible to soil factors under dodder parasitism. Meanwhile, the content of soil total nitrogen was significantly and positively correlated with the relative abundance of Alternaria in the rhizosphere and endosphere of soybean. Metabolomic analysis indicated that dodder parasitism altered the accumulation of flavonoids in soybean roots, with significant upregulation of the contents of kaempferol and its downstream derivatives under different parasitism conditions. Taken together, this study highlighted the important role of dodder parasitism in shaping the fungal communities and secondary metabolites associated with soybean roots, providing new insights into the mechanisms of multiple interactions among dodder, soybean, microbial communities and the soil environment.

Combined organic and inorganic pollutants can greatly impact crops and microbes, but the interaction between coexisted pollutants and their effects on root-associated microbes under flooding conditions remains poorly understood. In this study, greenhouse experiments were conducted to investigate the individual and combined effects of phenanthrene (PHE) and copper (Cu) on rice uptake and root-associated microbial coping strategies. The results showed that more than 90% of phenanthrene was degraded, while the existence of Cu significantly reduced the dissipation of PHE in the rhizosphere, and the coexistence of phenanthrene and copper promoted their respective accumulation in plant roots. Copper played a dominant role in the interaction between these two chemicals. Microbes that can tolerate heavy metals and degrade PAHs, e.g., Herbaspirillum , Sphingobacteriales, and Saccharimonadales, were enriched in the contaminated soils. Additionally, microbes associated with redox processes reacted differently under polluted treatments. Fe reducers increased in Cu-treated soils, while sulfate reducers and methanogens were considerably inhibited under polluted treatments. In total, our results uncover the combined effect of heavy metals and polycyclic aromatic hydrocarbons on the assemblage of root-associated microbial communities in anaerobic environments and provide useful information for the selection of effective root-associated microbiomes to improve the resistance of common crops in contaminated sites. [ABSTRACT FROM AUTHOR]

Crop root-associated microbiomes have been heralded for their potential to improve plant health and productivity. Optimizing beneficial interactions with rhizosphere microorganisms has been proposed to reduce reliance on external inputs, increase pathogen resistance, and alleviate abiotic stresses. Producers of Theobroma cacao, the economically important tropical perennial whose pods are used to produce chocolate, are faced with numerous challenges to sustainable production and rising demand. Cacao further provides an interesting case study to complement the extensive plant microbiome research on annual crops in temperate regions. However, current knowledge of the cacao root-associated microbiome is limited. Characterizing the factors that influence the composition and functions of microbial communities associated with cacao roots is a key first step to developing microbiome-targeted interventions for improved agricultural sustainability in cacao agroecosystems. These rhizosphere engineering approaches can be understood within the framework of provisioning, regulating, and supporting ecosystem services. Here we review the potential of cacao root-associated microbiomes to solve current challenges to production by increasing provisioning of ecosystem services. The major points are the following: (1) We describe factors affecting the cacao root-associated microbiome by expanding the traditional model of genotype-by-environment (G × E) interactions to include agricultural management (G × E × M) and discuss the unique aspects of this model in cacao agroforestry systems. (2) We then highlight how specific breeding targets and management practices can be optimized to enhance the ecosystem services mediated by the cacao root-associated microbiome. Such optimizations of ecosystem services will alleviate the reliance on external inputs and, eventually, contribute to more sustainable cacao production systems. [ABSTRACT FROM AUTHOR]

Combined organic and inorganic pollutants can greatly impact crops and microbes, but the interaction between coexisted pollutants and their effects on root-associated microbes under flooding conditions remains poorly understood. In this study, greenhouse experiments were conducted to investigate the individual and combined effects of phenanthrene (PHE) and copper (Cu) on rice uptake and root-associated microbial coping strategies. The results showed that more than 90% of phenanthrene was degraded, while the existence of Cu significantly reduced the dissipation of PHE in the rhizosphere, and the coexistence of phenanthrene and copper promoted their respective accumulation in plant roots. Copper played a dominant role in the interaction between these two chemicals. Microbes that can tolerate heavy metals and degrade PAHs, e.g., Herbaspirillum, Sphingobacteriales, and Saccharimonadales, were enriched in the contaminated soils. Additionally, microbes associated with redox processes reacted differently under polluted treatments. Fe reducers increased in Cu-treated soils, while sulfate reducers and methanogens were considerably inhibited under polluted treatments. In total, our results uncover the combined effect of heavy metals and polycyclic aromatic hydrocarbons on the assemblage of root-associated microbial communities in anaerobic environments and provide useful information for the selection of effective root-associated microbiomes to improve the resistance of common crops in contaminated sites.

Adoption of microbial consortia as plant growth-promoting microorganisms (PGPMs) instead of single-strain inoculants is discussed as an approach to increase the efficiency and flexibility of PGPM-assisted production strategies. This study provides the functional characterisation of a commercial microbial consortia product (MCP) in a series of greenhouse experiments with maize on a silty-loam field soil (pH 5.9). A 60%-increased abundance of bacteria that could be cultivated after rhizosphere extraction was measured after MCP inoculation at the end of the 42-days culture period. MCP inoculation did not stimulate shoot biomass production of maize fertilised with nitrate, but growth improvement was recorded in combination with stabilised ammonium, especially with reduced phosphorus (P) supply. The MCP inoculant improved the acquisition of ammonium-N but also increased shoot-P. MCP inoculation stimulated root length development under reduced P supply with stabilised ammonium by 52%. This was accompanied by the increased auxin production capacity of rhizosphere bacteria. C-, N-, and P-turnover in the rhizosphere were little affected by the MCP inoculation, as deduced from the analysis of activities of extracellular soil enzymes. The findings suggest that the form of N supply is crucial for the efficiency of plant-MCP interactions.

Root-microbiome interactions are of central importance for plant performance and yield. A distinctive feature of legumes is that they engage in symbiosis with N2-fixing rhizobia. If and how the rhizobial symbiotic capacity modulates root-associated microbiomes are still not yet well understood. We determined root-associated microbiomes of soybean inoculated with wild type (WT) or a noeI mutant of Bradyrhizobium diazoefficiens USDA 110 by amplicon sequencing. UPLC-MS/MS was used to analyze root exudates. The noeI gene is responsible for fucose-methylation of Nod factor secreted by USDA 110 WT strain. Soybean roots inoculated with the noeI mutant showed a significant decrease in nodulation and root-flavonoid exudation compared to roots inoculated with WT strain. The noeI mutant-inoculated roots exhibited strong changes in microbiome assembly in the rhizosphere and rhizoplane, including reduced diversity, changed co-occurrence interactions and a substantial depletion of root microbes. Root exudates and soil physiochemical properties were significantly correlated with microbial community shift in the rhizosphere between different rhizobial treatments. These results illustrate that rhizobial symbiotic capacity dramatically alters root-associated microbiomes, in which root exudation and edaphic patterns play a vital role. This study has important implications for understanding the evolution of plant-microbiome interactions.

Microplastics (MPs) from the incomplete degradation of agricultural mulch can stress the effectiveness of biofertilizers and ultimately affect the rhizosphere environment of crops. Yet, the involved mechanisms are poorly known and robust empirical data is generally lacking. Here, conventional polyethylene (PE) MPs and poly(butylene adipate-co-butylene terephthalate) (PBAT) / poly(lactic acid) (PLA) biodegradable MPs (PBAT-PLA BioMPs) were investigated to assess their potential impact on the rhizosphere environment of Brassica parachinensis in the presence of Bacillus amyloliquefaciens biofertilizer. The results revealed that both MPs caused different levels of inhibited crop both above- and belowground crop biomass (up to 50.11% and 57.09%, respectively), as well as a significant decrease in plant height (up to 48.63% and 25.95%, respectively), along with an imbalance of microbial communities. Transcriptomic analyses showed that PE MPs mainly affected root's vitamin metabolism, whereas PBAT-PLA BioMPs mainly interfered with the lipid's enrichment. Metabolomic analyses further indicated that PE MPs interfered with amino acid synthesis that involved in crops' oxidative stress, and that PBAT-PLA BioMPs mainly affected the pathways associated with root growth. Additionally, PBAT-PLA BioMPs had a bigger ecological negative impact than did PE MPs, as evidenced by more pronounced alterations in root antioxidant abilities, a higher count of identified differential metabolites, more robust interrelationships among rhizosphere parameters, and a more intricate pattern of impacts on rhizosphere metrics. This study highlights the MPs' impact on crop rhizosphere in a biofertilizer environment from a rhizosphere multi-omics perspective, and has theoretical implications for scientific application of biofertilizers. [Display omitted] • Both PE and PBAT-PLA BioMPs inhibited Brassica parachinensis growth. • MPs mainly affected rhizospheric bacterial communities and biodiversity. • MPs disrupted genes expression and related metabolic function in B. parachinensis. • PBAT-PLA BioMPs had bigger rhizosphere ecological responses than PE MPs. • The mulches' using with biofertilizer requires attention to rhizosphere profiles. [ABSTRACT FROM AUTHOR]

This study aims to better understand the relationship between the response to acid mine drainage (AMD) stress of tolerant plants and changes in root-related bacterial communities. In this study, reed stems were planted in AMD-polluted and unpolluted soils, and high-throughput sequencing was conducted to analyze the bacterial community composition in the soil, rhizosphere, rhizoplane and endosphere. The results showed that the effect of AMD pollution on root-associated bacterial communities was greater than that of rhizo-compartments. Proteobacteria were dominant across the rhizo-compartments between treatments. The microbiomes of unpolluted treatments were enriched by Alphaproteobacteria and Betaproteobacteria and depleted in Gammaproteobacteria ranging from the rhizoplane into the endosphere. However, the opposite trend was observed in the AMD pollution treatment, namely, Gammaproteobacteria were enriched, and Alphaproteobacteria and Deltaproteobacteria were mostly depleted. In addition, endophytic microbiomes were dominated by Comamonadaceae and Rhodocyclaceae in the unpolluted treatment and by Enterobacteriaceae in the AMD-polluted soils. PICRUSt showed that functional categories associated with membrane transport, metabolism and cellular processes and signaling processes were overrepresented in the endosphere of the AMD-polluted treatment. In conclusion, our study reveals significant variation in bacterial communities colonizing rhizo-compartments in two soils, indicating that plants can recruit functional bacteria to the roots in response to AMD pollution. [ABSTRACT FROM AUTHOR]

Adoption of microbial consortia as plant growth-promoting microorganisms (PGPMs) instead of singlestrain inoculants is discussed as an approach to increase the efficiency and flexibility of PGPM-assisted production strategies. This study provides the functional characterisation of a commercial microbial consortia product (MCP) in a series of greenhouse experiments with maize on a silty-loam field soil (pH 5.9). A 60%-increased abundance of bacteria that could be cultivated after rhizosphere extraction was measured after MCP inoculation at the end of the 42-days culture period. MCP inoculation did not stimulate shoot biomass production of maize fertilised with nitrate, but growth improvement was recorded in combination with stabilised ammonium, especially with reduced phosphorus (P) supply. The MCP inoculant improved the acquisition of ammonium-N but also increased shoot-P. MCP inoculation stimulated root length development under reduced P supply with stabilised ammonium by 52%. This was accompanied by the increased auxin production capacity of rhizosphere bacteria. C-, N-, and P-turnover in the rhizosphere were little affected by the MCP inoculation, as deduced from the analysis of activities of extracellular soil enzymes. The findings suggest that the form of N supply is crucial for the efficiency of plant-MCP interactions. [ABSTRACT FROM AUTHOR]

Antibiotics affect bacterial community structure and functions in soil. However, the response and adaptation of root-associated bacterial communities to antibiotic stress remains poorly understood. Here, rhizobox experiments were conducted with maize (Zea mays L.) upon exposure to antibiotics ciprofloxacin or tetracycline. High-throughput sequencing analysis of bacterial community and quantitative PCR analysis of nitrogen cycling genes show that ciprofloxacin and tetracycline significantly shift bacterial community structure in bulk soil, whereas plant host may mitigate the disturbances of antibiotics on bacterial communities in root-associated niches (i.e., rhizosphere and rhizoplane) through the community stabilization. Deterministic assembly, microbial interaction, and keystone species (e.g., Rhizobium and Massilia) of root-associated bacterial communities benefit the community stability compared with those in bulk soil. Meanwhile, the rhizosphere increases antibiotic dissipation, potentially reducing the impacts of antibiotics on root-associated bacterial communities. Furthermore, rhizospheric effects deriving from root exudates alleviate the impacts of antibiotics on the nitrogen cycle (i.e., nitrification, organic nitrogen conversion and denitrification) as confirmed by functional gene quantification, which is largely attributed to the bacterial community stability in rhizosphere. The present study enhances the understanding on the response and adaptation of root-associated bacterial community to antibiotic pollution. [Display omitted] • Antibiotics disturb structure and functions of soil bacterial community. • Responses of bacterial community to antibiotics vary between soil and root niches. • Plants mitigate disturbance of antibiotics on root-associated bacterial community. • Rhizosphere mitigates effects of antibiotics on nitrification and denitrification. • Root-associated bacteria strengthen community stability against antibiotic stress. [ABSTRACT FROM AUTHOR]

The effectiveness of biofertilizers as a cost-effective crop yield enhancer can be compromised by residual soil pollutants. However, the impact of accumulated polyadipate/butylene terephthalate microplastics (PBAT-MPs) from biodegradable mulch films on biofertilizer application and the consequent growth of crop plants remains unclear. Here, the effects of different levels of PBAT-MPs in soil treated with Bacillus amyloliquefaciens biofertilizer were assessed in a four-week potted experiment. PBAT-MPs significantly decreased the growth-promoting effect of the biofertilizer on Brassica chinensis L., resulting in a notable reduction in both above- and belowground biomass (up to 52.91% and 57.53%, respectively), as well as nitrate and crude fiber contents (up to 12.18% and 13.64%, respectively). In the rhizosphere microenvironment, PBAT-MPs increased soil organic carbon by 2.63-fold and organic matter by 2.68-fold, while enhancing sucrase (from 67.55% to 108.89%) and cellulase (from 31.26% to 49.10%) activities. PBAT-MPs also altered the rhizospheric bacterial community composition/diversity, resulting in more complex microbial networks. With regard to microbial function, PBAT-MPs impacted carbon metabolic function by inhibiting the 3-hydroxypropionate/4-hydroxybutyrate fixation pathway and influencing chitin and lignin degradation processes. Overall, the rhizospheric microbial profiles (composition, function, and network interactions) were the main contributors to plant growth inhibition. This study provides a practical case and theoretical basis for rational use of biodegradable mulch films and indicates that the residue of biodegradable films needs pay attention. [Display omitted] • PBAT-MPs attenuated the crop growth promotion effect of biofertilizers more then 50%. • PBAT-MPs changed the structure, function and network complexity of rhizospheric microbes. • PBAT-MPs inhibited carbon fixation/degradation efficience of soil microorganisms. • Scientific basis is necessary for the safe and rational use of biodegradable film mulch. [ABSTRACT FROM AUTHOR]

Understanding in population structure of a plant’s root-associated microbiome is applied in good practices in agricultural activities to improve production yields and enhance plant immune responses. The molecular analysis of bacterial populations inhabited in soil faces difficulties in obtaining high yield and high purity of DNA, and different commercial DNA extraction kits have been developed for this purpose. This study focuses on the comparison of DNA extraction of six different rice root-associated bacterial consortium using three commercial kits with two key technologies, spin-column adsorption and magnetic bead adsorption. The quality and quantity of genomic DNA obtained from these extraction methods were analyzed and compared based on DNA concentration, DNA purity and efficiency to be used as a template for 16sRNA amplification. The results showed that the extraction kit with magnetic bead adsorption technology showed the highest concentration (101.32 ng/μl) compared to other DNA extraction kits (32.67 and 1.89 ng/μl). The purity values (A260/A280) were assessed by using Nano-drop spectrophotometer and resulted in purities of nucleic acids in the range of 1.4-1.7. Thus, it was concluded that the extracted DNA obtained from the extraction kit with magnetic bead adsorption technology can be valuable for molecular analysis of microbial communities present in the soil.

The production and quality of Rehmannia glutinosa can be dramatically reduced by replant disease under consecutive monoculture. The root-associated microbiome, also known as the second genome of the plant, was investigated to understand its impact on plant health. Culture-dependent and culture-independent pyrosequencing analysis was applied to assess the shifts in soil bacterial communities in the rhizosphere and rhizoplane under consecutive monoculture. The results show that the root-associated microbiome (including rhizosphere and rhizoplane microbiomes) was significantly impacted by rhizocompartments and consecutive monoculture. Consecutive monoculture of R. glutinosa led to a significant decline in the relative abundance of the phyla Firmicutes and Actinobacteria in the rhizosphere and rhizoplane. Furthermore, the families Flavobacteriaceae, Sphingomonadaceae, and Xanthomonadaceae enriched while Pseudomonadaceae, Bacillaceae, and Micrococcaceae decreased under consecutive monoculture. At the genus level, Pseudomonas, Bacillus, and Arthrobacter were prevalent in the newly planted soil, which decreased in consecutive monocultured soils. Besides, culture-dependent analysis confirmed the widespread presence of Pseudomonas spp. and Bacillus spp. in newly planted soil and their strong antagonistic activities against fungal pathogens. In conclusion, R. glutinosa monoculture resulted in distinct root-associated microbiome variation with a reduction in the abundance of beneficial microbes, which might contribute to the declined soil suppressiveness to fungal pathogens in the monoculture regime. [ABSTRACT FROM AUTHOR]

Interactions between roots and microbes affect plant's resistance to abiotic stress. However, the structural and functional variation of root-associated microbiomes and their effects on metal accumulation in hyperaccumulators remain poorly understood. Here, we characterize the root-associated microbiota of a hyperaccumulating (HP) and a non-hyperaccumulating (NHP) genotype of Sedum alfredii by 16S ribosomal RNA gene profiling. We show that distinct microbiomes are observed in four spatially separable compartments: the bulk soil, rhizosphere, rhizoplane, and endosphere. Both the rhizosphere and rhizoplane were preferentially colonized by Proteobacteria, and the endosphere by Actinobacteria. The rhizosphere and endophytic microbiomes were dominated by the family of Sphingomonadaceae and Streptomycetaceae, respectively, which benefited for their survival and adaptation. The bacterial α-diversity decreases along the spatial gradient from the rhizosphere to the endosphere. Soil type and compartment were strongest determinants of root-associated community variation, and host genotype explained a small, but significant amount of variation. The enrichment of Bacteroidetes and depletion of Firmicutes and Planctomycetes in the HP endosphere compared with that of the NHP genotype may affect metal hyperaccumulation. Program PICRUSt predicted moderate functional differences in bacterial consortia across rhizocompartments and soil types. The functional categories involved in membrane transporters (specifically ATP-binding cassette transporters) and energy metabolism were overrepresented in endosphere of HP in comparison with NHP genotypes. Taken together, our study reveals substantial variation in structure and function of microbiomes colonizing different compartments, with the endophytic microbiota potentially playing an important role in heavy metal hyperaccumulation. [ABSTRACT FROM AUTHOR]

Organic pollutants influenced root-associated bacterial community. However, the response variation of root-associated bacterial community among different rice genotypes exposed to phthalates (PAEs) and their removal mechanism remains unknown. Here, bacterial community and PAE-degrading genes in root-associated niches were analyzed between low (Fengyousimiao) and high (Hhang) PAE-accumulating rice cultivars exposed to di-(2-ethylhexyl) phthalate (DEHP). DEHP dissipation percentages in rhizosphere of Hhang were significantly higher than those of Fengyousimiao. The bacterial community diversities (including Chao1 and Shannon index) significantly decreased along bulk soil - rhizosphere - rhizoplane - endosphere. The bacterial community structures were shaped mainly by root-associated niches, DEHP pollution and rice genotypes, with significant differences in rhizosphere and rhizoplane between Fengyousimiao and Hhang. Rhizosphere enriched more PAE-degrading bacteria than in bulk soil, and exhibited significantly higher expression of PAE-degrading genes (hydrolase 65, phtab, phtC, pcaF and pcaI) than in bulk soil. Furthermore, rhizosphere of Hhang demonstrated significantly stronger bacterial functions related to xenobiotics biodegradation and higher expression of PAE-degrading genes than those of Fengyousimiao , leading to significantly higher DEHP dissipation percentages in rhizosphere of Hhang. The findings demonstrate that Hhang shaped specific root-associated bacterial community with higher abundances of PAE-degrading bacteria and genes than Fengyousimiao to promote DEHP degradation. [Display omitted] • Higher DEHP dissipation occurred in rhizosphere of Hhang than that of Fengyousimiao. • Root-associated niches and DEHP pollution shaped more bacteria community than rice genotypes. • Root-associated bacteria had a strong adaptation potential under DEHP pollution. • Rhizosphere significantly enriched more PAE-degrading bacteria and genes than in bulk soil. • Hhang enriching more PAE-degrading bacteria and genes than Fengyousimiao enhanced DEHP degradation. [ABSTRACT FROM AUTHOR]

Co-contamination from both organic and inorganic pollutants is widely distributed in soils and is more difficult to remediate compared to single-type pollution. The co-planting pattern is an ideal phytoremediation strategy to remediate contaminated soils owing to their incomparable benefits originating from plant-plant interactions, but how to choose the best plant combinations and which factors affect the final remediating efficiency are still unclear. In this study, phytoremediation with different planting strategies of three herbaceous species, namely ryegrass (Lolium perenne), Dahurian wildrye (Elymus dahuricus), and Creeping bentgrass (Agrostis stolonifera), was conducted to remediate soils contaminated with both copper (Cu) and phenanthrene (PHE). The residual PHE content of all planting patterns was significantly lower compared to the unplanted bulk soil. More than 99% of total PHE losses were related to plant-stimulated microbial degradation, and plant intake was a minor pathway for PHE removal (accounting for less than 1%). The phytoextraction was the main Cu removal process by plants and the root uptake ability of Cu was the highest in Creeping bentgrass (an average of 708.9 mg kg−1) compared to the other two plants of ryegrass (an average of 269.9 mg kg−1) and Dahurian wildrye (an average of 268.0 mg kg−1). Two species co-planting combinations (ranging from an average of 264.4–302.3 mg m−2) greatly increased the total accumulated Cu content compared to single planting patterns (ranging from an average of 163.0–263.3 mg m−2). Combing the PHE removal results, the combination of Ryegrass x Creeping bentgrass, or Creeping bentgrass x Dahurian wildrye, where one species had a high biomass and the other species had a high uptake capacity, was a successful co-planting mode for the phytoremediation of multi-contaminated soils. Furthermore, microbes e.g. Massilia affiliated to Oxalobacteraceae, Sphingomonas affiliated to Sphingomonadaceae and Burkholderiaceae that can potentially degrade PAHs, as well as Rhizobium affiliated to Rhizobiaceae, Mucilaginibacter affiliated to Sphingobacteriaceae, and Caulobacter affiliated to Caulobacteraceae that can tolerate Cu stress were enriched in the rhizosphere. Overall, our study emphasizes the plant-plant interaction and the plant-microbe association, that both regulate phytoremediation effects on co-contaminated soils. [Display omitted] • Most of PHE losses were related to plant-stimulated microbial degradation. • Two species co-planting combinations increased the total accumulated Cu content. • Two plant species co-planting pattern was a successful phytoremediation strategy. • Microbes that can degrade PAHs or improve plant resistance were enriched. [ABSTRACT FROM AUTHOR]

Plant root-associated microbiomes play critical roles in promoting plant health, productivity, and tolerance to biotic/abiotic stresses. Blueberry (Vaccinium spp.) is adapted to acidic soils, while the interactions of the root-associated microbiomes in this specific habitat under various root microenvironments remain elusive. Here, we investigated the diversity and community composition of bacterial and fungal communities in various blueberry root niches (bulk soil, rhizosphere soil, and root endosphere). The results showed that blueberry root niches significantly affected root-associated microbiome diversity and community composition compared to those of the three host cultivars. Deterministic processes gradually increased along the soil-rhizosphere-root continuum in both bacterial and fungal communities. The co-occurrence network topological features showed that both bacterial and fungal community complexity and intensive interactions decreased along the soil-rhizosphere-root continuum. Different compartment niches clearly influenced bacterial-fungal interkingdom interactions, which were significantly higher in the rhizosphere, and positive interactions gradually dominated the co-occurrence networks from the bulk soil to the endosphere. The functional predictions showed that rhizosphere bacterial and fungal communities may have higher cellulolysis and saprotrophy capacities, respectively. Collectively, the root niches not only affected microbial diversity and community composition but also enhanced the positive interkingdom interactions between bacterial and fungal communities along the soil-rhizosphere-root continuum. This provides an essential basis for manipulating synthetic microbial communities for sustainable agriculture. IMPORTANCE The blueberry root-associated microbiome plays an essential role in its adaptation to acidic soils and in limiting the uptake of soil nutrients by its poor root system. Studies on the interactions of the root-associated microbiome in the various root niches may deepen our understanding of the beneficial effects in this particular habitat. Our study extended the research on the diversity and composition of microbial communities in different blueberry root compartment niches. Root niches dominated the root-associated microbiome compared to that of the host cultivar, and deterministic processes increased from the bulk soil to the endosphere. In addition, bacterial-fungal interkingdom interactions were significantly higher in the rhizosphere, and those positive interactions progressively dominated the co-occurrence network along the soil-rhizosphere-root continuum. Collectively, root niches dominantly affected the root-associated microbiome and the positive interkingdom interactions increased, potentially providing benefits for the blueberry., Competing Interests: The authors declare no conflict of interest.

Many microorganisms are found in the roots of plants, and are important for plant growth, nutrition uptake, and disease prevention. While the microorganisms of many crops such as soybean, rice, and maize have been studied, the root-associated microbial diversity of horticultural plants such as Paeonia lactiflora has been little studied. In this study, we investigated the composition, abundance, diversity and variability of microorganisms associated with different rhizospheric compartments (bulk soil, rhizosphere, rhizoplane, root endosphere) of different cultivars of P. lactiflora. We used the root and root-associated soil of a medicinal cultivar P. lactiflora cv 'Hang Baishao' (HS, 2n = 10) and an ornamental cultivar P. lactiflora cv 'Zi Fengyu' (ZFY, 2n = 10) as our study objectives. Based on Illumina Novaseq 6000 high-throughput sequencing, the 16S rRNA V4 amplicon of two cultivars of P. lactiflora root-associated bacterial communities and the ITS1-spanning amplicon of the fungal communities were sequenced, and the microbial communities were analyzed for relevant bioinformatics. Observed Species, Simpson, Shannon, and Chao1 indices showed that the microbial diversity of the rhizosphere was greater than that of the root, with the with the diversity decreasing from the bulk soil to the root endosphere. In addition, Cyanobacteria and Proteobacteria were the most abundant of the root-associated bacterial communities, accounting for 19.59 % and 31.23 %, respectively. On the other hand, Ascomycota (37.74 %) and Basidiomycota (11.15 %) were the most dominant fungal communities in the four root-associated compartments. Compared to ZFY, the root-associated compartments of HS were able to enrich more functional bacteria associated with bacterial inhibition, such as Kribbella , Actinophytocola and Actinoallomurus. This study explored the complex root microflora structure of P. lactiflora and provided a theoretical basis for future studies on the synthetic microbial community of soil. [ABSTRACT FROM AUTHOR]

Strongly acidic soils are characterized by high aluminum (Al) toxicity and low phosphorus (P) availability, which suppress legume plant growth and nodule development. Arbuscular mycorrhizal fungi (AMF) stimulate rhizobia and enhance plant P uptake. However, it is unclear how this symbiotic soybean-AMF-rhizobial trio promotes soybean growth in acidic soils. We examined the effects of AMF and rhizobium addition on the growth of two soybean genotypes, namely, Al-tolerant and Al-sensitive soybeans as well as their associated bacterial and fungal communities in an acidic soil. With and without rhizobial addition, AMF significantly increased the fresh shoot and root biomass of Al-tolerant soybean by 47%/87% and 37%/24%, respectively. This increase in plant biomass corresponded to the enrichment of four plant growth-promoting rhizobacteria (PGPR) in the rhizospheric soil, namely, Chitinophagaceae bacterium 4GSH07, Paraburkholderia soli, Sinomonas atrocyanea, and Aquincola tertiaricarbonis. For Al-sensitive soybean, AMF addition increased the fresh shoot and root biomass by 112%/64% and 30%/217%, respectively, with/without rhizobial addition. Interestingly, this significant increase coincided with a decrease in the pathogenic fungus Nigrospora oryzae as well as an increase in S. atrocyanea , A. tertiaricarbonis , and Talaromyces verruculosus (a P-solubilizing fungus) in the rhizospheric soil. Lastly, the compartment niche along the soil-plant continuum shaped microbiome assembly, with pathogenic/saprotrophic microbes accumulating in the rhizospheric soil and PGPR related to nitrogen fixation or stress resistance (e.g., Rhizobium leguminosarum and Sphingomonas azotifigens) accumulating in the endospheric layer. IMPORTANCE Taken together, this study examined the effects of arbuscular mycorrhizal fungi (AMF) and rhizobial combinations on the growth of Al-tolerant and Al-sensitive soybeans as well as their associated microbial communities in acidic soils and concluded that AMF enhances soybean growth and Al stress tolerance by recruiting PGPR and altering the root-associated microbiome assembly in a host-dependent manner. In the future, these findings will help us better understand the impacts of AMF on rhizosphere microbiome assembly and will contribute to the development of soybean breeding techniques for the comprehensive use of PGPR in sustainable agriculture.

Root-associated microbiomes are essential for the ecological function of the root system. However, their assembly mechanisms in wetland are poorly understood. In this study, we explored and compared the ecological processes of bacterial and fungal communities in water, bulk soil, rhizosphere soil, and root endosphere niches for 3 developmental stages of Typha orientalis at different wetland sites, and assessed the potential functions of root endosphere microbiomes with function prediction. Our findings suggest that the microbial diversity, composition, and interaction networks along the water-soil-plant continuum are shaped predominantly by compartment niche and developmental stage, rather than by wetland site. Source tracking analysis indicated that T. orientalis' root endosphere is derived primarily from the rhizosphere soil (bacteria 39.9%, fungi 27.3%) and water (bacteria 18.9%, fungi 19.1%) niches. In addition, we found that the assembly of bacterial communities is driven primarily by deterministic processes and fungal communities by stochastic processes. The interaction network among microbes varies at different developmental stages of T. orientalis , and is accompanied by changes in microbial keystone taxa. The functional prediction data supports the distribution pattern of the bacterial and fungal microbiomes, which have different ecological roles at different plant developmental stages, where more beneficial bacterial taxa are observed in the root endosphere in the early stages, but more saprophytic fungi in the late stages. Our findings provide empirical evidence for the assembly, sources, interactions, and potential functions of wetland plant root microbial communities and have significant implications for the future applications of plant microbiomes in the wetland ecosystem. IMPORTANCE Our findings provide empirical evidence for the assembly, sources, interactions, and potential functions of wetland plant root microbial communities, and have significant implications for the future applications of plant microbiomes in the wetland ecosystem.

The degradable plastic poly(butylene adipate-co-terephthalate) (PBAT) is considered a potential replacement for low-density polyethylene (LDPE) as the main component of mulch film. However, it is not clear whether PBAT is harmful to the plant-soil system. Thus, we determined the effects of LDPE microplastics (LDPE-MPs) and PBAT microplastics (PBAT-MPs) on the growth of Arabidopsis. The inhibitory effect of PBAT-MPs was greater than that of LDPE-MPs on the growth of Arabidopsis. Transcriptome analysis showed that PBAT-MPs severely disrupted the photosynthetic system of Arabidopsis and increased the expression levels of genes in drug transport-related pathways. PBAT-MPs increased the relative abundances of Bradyrhizobium , Hydrogenophaga , and Arthrobacter in the bulk soil and rhizosphere soil. The abundances of Variovorax , Flavobacterium , and Microbacterium increased in the plant root zone only under PBAT-MPs. Functional prediction analysis suggested that microorganisms in the soil and plant root zone could degrade xenobiotics. Furthermore, the degradation products from PBAT comprising adipic acid, terephthalic acid, and butanediol were more toxic than PBAT-MPs. Our findings demonstrate that PBAT-MPs may be degraded by microorganisms to produce chemicals that are highly toxic to plants. Thus, biodegradable plastics may pose a great risk to the environment. [Display omitted] • Toxic effects of PBAT-MPs greater than those of LDPE-MPs on growth of Arabidopsis. • Expression levels of genes in Arabidopsis photosynthetic system severely disrupted by PBAT-MPs. • PBAT-MPs altered microbial community structure and functions in the bulk soil, rhizosphere soil, and plant root zone. • Degradation products from PBAT comprising adipic acid, phthalic acid, and butanediol toxic in Arabidopsis. [ABSTRACT FROM AUTHOR]

Plant root-associated microbiome can be influenced by environmental stress like pollution. However, how organic pollution influences microbial communities in different root-associated niches and plant-microbe interaction remains unclear. We analyzed maize root-associated bacterial communities under stress of di-(2-ethylhexyl) phthalate (DEHP). The results demonstrate that structures and functions of bacterial communities are significantly different among four root-associated niches, and bacterial diversities gradually decline along bulk soil - rhizosphere - rhizoplane - endosphere. DEHP stress significantly reduces bacterial community diversities in both rhizosphere and rhizoplane, and changes their composition, enrichment and depleting process. DEHP stress led to the enrichment of some specific bacterial taxa like phthalate-degrading bacteria (e.g., Rhizobium and Agromyces) and functional genes involving in phthalate degradation (e.g., pht3 and pcaG). Notably, rhizoplane bacterial community is more sensitive to DEHP stress by enriching stress-resistant bacteria and more complex microbial network on rhizoplane than in rhizosphere. DEHP stress also disturbs the colonization and biofilm forming of root-associated bacteria on rhizoplane. Rhizoplane bacterial community is significantly correlated with maize growth while negatively influenced by DEHP stress. DEHP stress negatively influences plant-microbe interaction and inhibits maize growth. This study provides deep and comprehensive understanding for root-associated bacterial community in response to organic pollution. [Display omitted] • Distinct response variation occurred in root-associated bacterial community to phthalate pollution. • Pollution effect on rhizoplane microbiome was proved by synthetic bacterial community. • Structure and functions of rhizoplane microbiome are more sensitive to phthalate stress. • Phthalate negatively influenced rhizoplane microbiome and inhibited maize growth. • Phthalate disturbed colonization and assembly of root-associated bacteria on rhizoplane. [ABSTRACT FROM AUTHOR]

Root-microbiome interactions are of central importance for plant performance and yield. A distinctive feature of legumes is that they engage in symbiosis with N 2 -fixing rhizobia. If and how the rhizobial symbiotic capacity modulates root-associated microbiomes are still not yet well understood. We determined root-associated microbiomes of soybean inoculated with wild type (WT) or a noeI mutant of Bradyrhizobium diazoefficiens USDA 110 by amplicon sequencing. UPLC-MS/MS was used to analyze root exudates. The noeI gene is responsible for fucose-methylation of Nod factor secreted by USDA 110 WT strain. Soybean roots inoculated with the noeI mutant showed a significant decrease in nodulation and root-flavonoid exudation compared to roots inoculated with WT strain. The noeI mutant-inoculated roots exhibited strong changes in microbiome assembly in the rhizosphere and rhizoplane, including reduced diversity, changed co-occurrence interactions and a substantial depletion of root microbes. Root exudates and soil physiochemical properties were significantly correlated with microbial community shift in the rhizosphere between different rhizobial treatments. These results illustrate that rhizobial symbiotic capacity dramatically alters root-associated microbiomes, in which root exudation and edaphic patterns play a vital role. This study has important implications for understanding the evolution of plant-microbiome interactions., Competing Interests: The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest., (Copyright © 2021 Liu, Ma, Chen, Schlaeppi, Erb, Stirling, Hu, Wang, Zhang, Zhao, Lu, Ye and Xu.)

• The correlation between bioactive compounds and rhizosphere microbiome in P. cuspidatum. • The Stenotrophomonas was specifically enriched in the root endosphere. • Bcteroides , and Erysipelatoclostridium might promote resveratrol synthesis. Polygonum cuspidatum (Polygonum cuspidatum Sieb. & Zucc.), a medicinal plant that is abundantly accumulating bioactive compounds in its roots, is the primary source of resveratrol in industry and has long been recognized as raw materials for traditional Chinese medicine. Plant root secondary metabolism is correlated to its surrounding microbial communities. However, the root-associated microbiomes of P. cuspidatum and the potential correlation between the bioactive compounds and microbiomes are poorly understood. To unveil the root-associated bacterial community, the microbiome compositions of P. cuspidatum roots across four cultivation years were analyzed by using 16S rRNA gene sequencing. Furthermore, the relationships among root-associated bacteria, soil properties, and four major bioactive compounds (polydatin, resveratrol, emodin, and physcion) were explored by a multivariate correlation study. The composition of the rhizosphere microbiome significantly differed from that of the endosphere microbiome. The composition of the rhizosphere microbiome significantly varied across different cultivation years and soil properties, contributing to the majority of variance. Regarding different cultivation years and soil properties, the compositions of the root endosphere microbiome remained relatively stable, indicating a strong selection effect in P. cuspidatum roots. Among root endosphere microbes, Stenotrophomonas was specifically enriched from rhizosphere with a 15 times increase of relative abundance, exhibiting no significant variation across different cultivation years. The relative abundance of rhizosphere Stenotrophomonas was positively correlated with the content of emodin. Taken together, this study demonstrated that the stability of the root endosphere microbiome with a dominance of Stenotrophomonas may maintain the growth of P. cuspidatum through the combined effect of emodin. The contents of bioactive compounds in roots exhibited distinct correlations with specific bacteria, suggesting that Bacteroides , Acinetobacter , Erysipelatoclostridium , and Achromobacter may enhance the accumulation of resveratrol. This study provides insights into the interaction networks among P. cuspidatum root-associated bacteria, cultivation years, soil properties, and bioactive compounds, giving us a new opportunity to manipulate the production of bioactive compounds, and thus improve the industrial and medicinal value of P. cuspidatum in future. [ABSTRACT FROM AUTHOR]