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Plant microbiota are an important factor impacting plant cadmium (Cd) uptake. However, little is known about how plant microbiota affects the Cd uptake by plants under the influence of microplastics (MPs) with different particle sizes. In this study, bacterial structure and assembly in the rhizosphere and endosphere in pakchoi were analyzed by amplicon sequencing of 16S rRNA genes under the influence of different particle sizes of polystyrene microplastics (PS-MPs) combined with Cd treatments. Results showed that there were no significant differences observed in the shoot endophytes among different treatments. However, compared to Cd treatment, larger-sized PS-MPs (2 and 20 μm) significantly increased community diversity and altered the structural composition of rhizosphere bacteria and root endophytes, while smaller-sized PS-MPs (0.2 μm) did not. Under the treatment of larger-sized PS-MPs, the niche breadth of rhizosphere bacteria and root endophytes were significantly increased. And larger-sized PS-MPs also maintained stability and complexity of bacterial co-occurrence networks, while smaller-sized PS-MPs reduced them. Furthermore, compared to Cd treatment, the addition of larger particle size PS-MPs decreased the proportion of homogeneous section, while increased the proportion of drift in root endophytic bacterial community assembly. The role of larger-sized MPs in the community assembly of rhizosphere bacteria was opposite. Using random forest and structural equation models, the study found that larger-sized PS-MPs can promote the colonization of specific bacterial taxa, such as Brevundimonas, AKAU4049, SWB02, Ellin6055, Porphyrobacter, Sphingorhabdus, Rhodobacter, Erythrobacter, Devosia and some other bacteria belonging to Alphaproteobacteria, in the rhizosphere and root endosphere. The colonization of these taxa can may induce the formation of biofilms in the roots, immobilize heavy metals through oxidation processes, and promote plant growth, thereby reducing Cd uptake by pakchoi. The findings of this study provide important insights into the microbial mechanisms underlying the influence of MPs with different particle sizes on plant Cd uptake.

Rhizosphere bacteria are critical for supporting plant performance in stressful environments. Understanding the assembly and co-occurrence of rhizosphere bacterial communities contributes significantly to both plant growth and heavy metal accumulation. In this study, Ligustrum lucidum and Melia azedarach were planted in soils with simulated varying levels of Pb-Zn contamination. The Rhizosphere bacterial communities were investigated by using 16S rRNA gene sequencing. The impacts of Pb-Zn contamination on the diversity and structure of the rhizosphere bacterial community were found to be greater than those of both tree species. The variation in bacterial community structure in both trees was mainly driven by the combinations of Pb-Zn and soil properties. Deterministic processes (non-planted, 82 %; L. lucidum, 73 %; M. azedarach, 55 %) proved to be the most important assembly processes for soil bacterial communities, but both trees increased the importance of stochastic processes (18 %, 27 %, 45 %). The rhizosphere co-occurrence networks exhibited greater stability compared to the non-planted soil networks. Rare taxa played a dominant role in maintaining the stability of rhizosphere networks, as most of the keystone taxa within rhizosphere networks belonged to rare taxa. Dissimilarities in the structure and network complexity of rhizosphere bacterial communities were significantly associated with differences in tree biomass and metal accumulation. These variations in response varied between both trees, with L. lucidum exhibiting greater potential for phytoremediation in its rhizosphere compared to M. azedarach. Our results offer valuable insights for designing effective microbe-assisted phytoremediation systems., Competing Interests: Declaration of Competing Interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2024 Elsevier B.V. All rights reserved.)

Microbial communities colonize plant tissues and contribute to host function. How these communities form and how individual members contribute to shaping the microbial community are not well understood. Synthetic microbial communities, where defined individual isolates are combined, can serve as valuable model systems for uncovering the organizational principles of communities. Using genome-defined organisms, systematic analysis by computationally-based network reconstruction can lead to mechanistic insights and the metabolic interactions between species. In this study, 10 bacterial strains isolated from the Populus deltoides rhizosphere were combined and passaged in two different media environments to form stable microbial communities. The membership and relative abundances of the strains stabilized after around 5 growth cycles and resulted in just a few dominant strains that depended on the medium. To unravel the underlying metabolic interactions, flux balance analysis was used to model microbial growth and identify potential metabolic exchanges involved in shaping the microbial communities. These analyses were complemented by growth curves of the individual isolates, pairwise interaction screens, and metaproteomics of the community. A fast growth rate is identified as one factor that can provide an advantage for maintaining presence in the community. Final community selection can also depend on selective antagonistic relationships and metabolic exchanges. Revealing the mechanisms of interaction among plant-associated microorganisms provides insights into strategies for engineering microbial communities that can potentially increase plant growth and disease resistance. Further, deciphering the membership and metabolic potentials of a bacterial community will enable the design of synthetic communities with desired biological functions.

Production of brinjal (Solanum melongena L.) is considerably reduced by infestations of root-knot nematodes (RKN). As chemical pesticides are increasingly being regulated globally, scientists are focusing on biorational management. An experiment was undertaken to screen resistant brinjal cultivars in Bangladesh against Meloidogyne javanica in a pot trial. Pot and field trials were also conducted to evaluate the efficacy and profitability of individual and combined applications of several biorational components to manage M. javanica on brinjal. Of twenty brinjal cultivars screened, cv. Noagram was found ‘moderately resistant’ and others were ‘susceptible’ to ‘highly susceptible’ against M. javanica. In both pot and field trials, most of the growth parameters of brinjal and reproductive parameters of M. javanica were significantly different than the control for both the individual and combined treatments of different biorational components which included cabbage, marigold, vermicompost, biogas digestate, Bacillus subtilis and Pseudomonas fluorescens. The yield was significantly higher for the combined treatments than the individual applications. The benefit-cost ratio (BCR) differed among the treatments. The highest yield (29.5 t/ha) and BCR (3.67) with the lowest reproductive factor (0.33) was obtained by the combined application of biogas digestate and B. subtilis. This is the first report on the efficiency and profitability assessment of biogas digestate in combination with a bio-agent in addressing the management of RKN, which might be very important considering the global concern of environmental pollution. The cultivar Noagram might be a potential source of resistant genes in brinjal against M. javanica.

Understanding the responses of soybean rhizosphere and functional microbiomes in intercropping scenarios holds promise for optimizing nitrogen utilization in legume-based intercropping systems. This study investigated three cropping layouts under film mulching: sole soybean (S), soybean-maize intercropping in one row (IS), and soybean-maize intercropping in two rows (IIS), each subjected to two nitrogen levels: 110 kg N ha -1 (N110) and 180 kg N ha -1 (N180). Our findings reveal that cropping patterns alter bacterial and nifh communities, with approximately 5 % of soybean rhizosphere bacterial amplicon sequence variants (ASVs) and 42 % of rhizosphere nifh ASVs exhibiting altered abundances (termed sensitive ASVs). Root traits and soil properties shape these communities, with root traits exerting greater influence. Sensitive ASVs drive microbial co-occurrence networks and deterministic processes, predicting 85 % of yield variance and 78 % of partial factor productivity of nitrogen, respectively. These alterations impact bacterial and nifh diversity, complexity, stability, and deterministic processes in legume-based intercropping systems, enhancing performance in terms of yield, nitrogen utilization efficiency, land equivalent ratio, root nodule count, and nodule dry weight under IIS patterns with N110 compared to other treatments. Our findings underscore the importance of field management practices in shaping rhizosphere-sensitive ASVs, thereby altering microbial functions and ultimately impacting the productivity of legume-based intercropping systems. This mechanistic understanding of soybean rhizosphere microbial responses to intercropping patterns offers insights for sustainable intercropping enhancements through microbial manipulation., Competing Interests: Declaration of competing interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2024 Elsevier B.V. All rights reserved.)

Lead (Pb) contamination presents a widespread environmental plague. Sedum alfredii is widely used for soil phytoremediation owing to its capacity to extract heavy metals, such as Pb. Although efficient Pb extraction is mediated by complex interactions between the roots and rhizospheric bacteria, the mechanism by which S. alfredii recruits microorganisms under Pb stress remains unclear. The Pb-accumulating ecotype (AE) and non-accumulating ecotype (NAE) of S. alfredii recruited different rhizobacterial communities. Under Pb stress, AE rhizosphere-enriched bacteria assembled into stable-connected clusters with higher phylogenetic and functional diversity. These microbes, e.g., Flavobacterium, could release indoleacetic acid to promote plant growth and siderophores, thereby increasing Pb availability. The NAE rhizosphere-enriched functional bacteria “desperately” assembled into highly specialized functional clusters with extremely low phylogenetic diversity. These bacteria, e.g., Pseudomonas, could enhance phosphorus solubilization and Pb precipitation, thereby reducing Pb stress and plant Pb accumulation. High niche overlap level of the rhizo-enriched species raised challenges in soil resource utilization, whereas the NAE community assembly was markedly constrained by environmental “selection effect” than that of AE rhizobacterial community. These results indicate that different ecotypes of S. alfredii recruit distinct bacterial functional assemblies to drive specific plant-soil feedbacks for different survival in Pb-contaminated soils. To cope with heavy metal stress, NAE formed a highly functional and specialized but vulnerable community and efficiently blocked heavy metal absorption by plants. However, the AE community adopted a more stable and elegant strategy to promote plant growth and the accumulation of dry matter via multiple evolutionary strategies that ensured a high yield of heavy metal phytoextraction. This for the first time provides new insights into the roles of rhizosphere microbes in plant adaptations to abiotic stresses.

Interactions between plants and soil microbes are important to plant hybrid breeding under global change. However, the relationship between host plants and rhizosphere soil microorganisms has not been fully elucidated. Understanding the rhizosphere microbial structure of parents and progenies would provide a deeper insight into how genetic effects modulate the relationship between plants and soil. In this study, two family groups of poplar trees (A: parents and their two progenies; B: parents and their one progeny) with different genetic backgrounds (including seven genotypes) were selected from a common garden, and their rhizobacterial communities were analyzed to explore parent-progeny relationships. Our results showed significant differences in phylogenetic diversity, the number of 16S genes and the structure of rhizosphere bacterial communities (Adonis: R 2  = 0.166, P < 0.01) between different family groups. Rhizosphere bacterial community structure was significantly dominated by genetic effects. Compared with abundant taxa, genetic effects were more powerful drivers of rare taxa. In addition, bacterial communities of hybrid progenies were all significantly more similar to their parents compared to the other group of parents, especially among rare taxa. The two poplar family groups exhibited differences between their rhizosphere bacterial co-occurrence networks. Group B had a relatively complex network with 2380 edges and 468 nodes, while group A had 1829 edges and 304 nodes. Soil organic carbon and carbon to nitrogen ratio (C/N) also influenced the rhizosphere bacterial community assembly. This was especially true for soil C/N, which explained 23 % of the β-nearest taxon index (βNTI) variation in rare taxa. Our results reveal the relationship of rhizosphere microorganisms between parents and progenies. This can help facilitate an understanding of the combination of plant breeding with microbes resource utilization and provide a theoretical basis for scientific advancement to support the development of forestry industry., Competing Interests: Declaration of competing interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2023 Elsevier B.V. All rights reserved.)

Aromatic plants, such as vetiver grass (Chrysopogon zizanioides), possess strong abilities to resist environmental stresses. However, whether such abilities stem from the interaction between specific chemical characteristics and the associated microbes in roots and rhizosphere remains unclear. We conducted pot experiments to analyze stress-tolerant parameters, organic compounds, and bacterial communities in roots and rhizosphere of vetiver under typical metal(loid) stress [cadmium (Cd), arsenic (As), or Cd + As] over time. The results showed that the vetiver displayed limited toxic symptoms in terms of oxidative stress-antioxidant balance and chlorophyll content. The root low-molecular-weight organic acids (LMWOAs), fatty acids, and sterols were highly sensitive to growth stage (increased from the 4-month to the 8-month stage), and less sensitive to metal(loid) stress. The sugar contents in the rhizosphere soils also notably increased over time. Such endo and rhizosphere chemical changes strongly correlated with and enriched the functional bacteria including Streptomyces, which can resist stress and promote plant growth. The compound-bacteria interaction highly depended on growth stage. Vetiver demonstrated a progressive adaptation to stresses through metabolite modulation and cellular defense reinforcement. Our study evidenced that vetiver shapes the interaction between organic compounds and bacterial community in the root-soil interface and provides notable stress-resistant functions., Competing Interests: Declaration of Competing Interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2023 Elsevier B.V. All rights reserved.)

Recently, the environmental and agricultural impact of plastic waste has attracted considerable attention. Here, we investigated the impact of sub-micron polyethylene (PE) and polypropylene (PP) microplastics (MPs) on nitrogen cycling, with emphasis on bacterial abundance and diversity in a soil-soybean (Glycine max) system. Exposure to soil containing MPs (50 and 500 mg kg -1 ) did not affect soybean growth, but significantly increased plant nitrogen uptake, which was confirmed by increased activities of nitrogenase in the soil and glutamine synthetase in soybean root. Additionally, there was an increase in 16S gene copy number and carbon and nitrogen substrate utilization, indicating increased abundance and activity of rhizosphere microbial communities. Moreover, MP contamination affected the taxonomic profile of rhizosphere bacteria, especially the abundance of symbiotic and free-living bacteria involved in nitrogen cycling. Furthermore, qPCR analysis of nitrogen-related genes and Kyoto Encyclopedia of Genes and Genomes analysis of 16S rRNA gene sequencing data revealed an increased abundance of functional genes associated with nitrogen fixation and nitrification. However, the concentration and polymer type of MPs did not have a significant impact in our system. Overall, these results provide insights into the interactions between MPs and rhizosphere bacterial communities in the soil-legume system., Competing Interests: Declaration of Competing Interest The authors declare the following financial interests/personal relationships which may be considered as potential competing interests: Hakwon Yoon reports financial support was provided by National Research Foundation of Korea. June-Woo Park reports financial support was provided by National Research Council of Science and Technology. June-Woo Park reports financial support was provided by Korea Institute of Toxicology., (Copyright © 2023 The Authors. Published by Elsevier B.V. All rights reserved.)

8:2 fluorotelomer carboxylic acid (8:2 FTCA), an important precursor of perfluorocarboxylic acids (PFCAs), is widely detected in environment and biotas. Hydroponic exposures were conducted to investigate the accumulation and metabolism of 8:2 FTCA in wheat (Triticum aestivum L.) and pumpkin (Cucurbita maxima L.). Endophytic and rhizospheric microorganisms co-existing with the plants were isolated to investigate their contributions to degrade 8:2 FTCA. Wheat and pumpkin roots could take up 8:2 FTCA efficiently with the root concentration factor (RCF) as 5.78 and 8.93, respectively. 8:2 FTCA could be biotransformed to 8:2 fluorotelomer unsaturated carboxylic acid (8:2 FTUCA), 7:3 fluorotelomer carboxylic acid (7:3 FTCA), and seven PFCAs with 2-8 carbon chain length in plant roots and shoots. Cytochromes P450 (CYP450) and glutathione-S-transferase (GST) activities in plants were significantly increased, while flavin-dependent monooxygenases (FMOs) activities were not changed, suggesting that CYP 450 and GST were involved in the transformation of 8:2 FTCA in plant tissues. Twelve 8:2 FTCA-degrading endophytic (8 strains) and rhizospheric (4 strains) bacterial strains were isolated from root interior, shoot interior and rhizosphere of plants, respectively. These bacteria were identified as Klebsiella sp. based on the morphology and 16S rDNA sequence, and they could biodegrade 8:2 FTCA to intermediates and stable PFCAs., Competing Interests: Declaration of Competing Interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2023 Elsevier B.V. All rights reserved.)

We present the complete genome sequence of Luteibacter rhizovicinus type strain LJ96T, a yellow-pigmented gammaproteobacterium isolated from the rhizosphere of barley (Hordeum vulgare) Johansen et al. (2005) , a species with numerous potential applications. The genome sequence was deposited to NCBI GenBank with the accession number CP017480.

Pond-ditch circulation system (PDCS) is a promising remediation strategy for rural wastewater treatment. Aquatic plants play nonnegligible roles in the nutrient removal of the PDCS. However, mechanisms of root exudates regulating nutrient removal in PDCSs remained unclear. In our study, the PDCS achieved higher total nitrogen (TN) and phosphorus (TP) removal rates (72.7-97.4%) compared to the static system. Protein contents in root exudates of the PDCS ranged from 0.041 to 1.332 mg L -1 , showing negative associations with Simpson index. Lactic acid and tartaric acid in the PDCS varied from 0.045 to 0.380 mg L -1 and 0.024 to 5.446 mg L -1 , which were tightly linked with TN, TP, and TP removal rates and most sediment properties, especially sediment total nitrogen (STN) and total organic carbon (TOC), and sediment inorganic phosphorus (SIP). Moreover, the top 3 relative dominant genus were Bacillus (0.11%-17.90%), Geobacter (0.35%-12.04%), and Clostridium sensu stricto 1 (0.14%-12.05%), which might be the predominant groups in nutrient removal of PDCSs. RDA results indicated that lactic acid, protein, and amino acids were positively correlated with Geobacter; while Bacillus was significantly affected by water content. Path analysis further demonstrated that the indirect effect of secretion from plant roots on nutrient removal rates was mainly through modulating bacteria diversity and relative abundance. Taken together, root exudates, especially protein, amino acids, and lactic acid, altered rhizosphere microbial relative abundance and diversity, where the impacts were bacterial species-dependent., Competing Interests: Declaration of competing interest The authors declare that no conflict of interest exists., (Copyright © 2021. Published by Elsevier B.V.)

Soil pH is an important predictor of bacterial community composition and diversity. Examining the effects of pH on diversity, structure, interaction, and function of rhizosphere bacterial communities in acidic crop soils provide valuable information for knowing potential role of rhizosphere bacteria in crop yield. Here, we collected soils from artificial greenhouses and applied Illumina Miseq sequencing, quantitative PCR techniques, multiple ecological analysis methods, including topological analysis and functional profiling to analyze our data and validate our hypotheses. We found that the soil physicochemical properties, species diversity, and rhizosphere bacterial community composition were significantly affected by the degree of soil acidification (pH < 5.5 and pH > 5.5) but not vegetation type. Additionally, bacterial absolute abundance increased with higher pH. The 18 soil samples were clustered into two distinct groups of pH < 5.5 and pH > 5.5 at the OTU level, and soil pH had more of an effect on bacterial community composition compared to the other physicochemical variables. In addition, rhizosphere bacteria might presented relatively less competition for survival in pH < 5.5 soils, and bacterial community functions, including nutrient (i.e., carbon, nitrogen, phosphorus, and sulphur) cycling-related enzymes and proteins, were downregulated in more acidic soils (pH < 5.5) based on sequence analysis. To our knowledge, this report is the first to show that pH is a key factor affecting the diversity, structure, interaction, and function of rhizosphere bacterial communities in acidic crop soil in artificial greenhouses. Our findings emphasize that community function and structure of rhizosphere bacteria are closely correlated in more acidic soils, and the decreased crop yield may be correlated with attenuation of the function of the rhizosphere bacterial community., (Copyright © 2019 Elsevier B.V. All rights reserved.)

The molecular structure of soil organic matter (SOM) is closely related to the structure and functions of the rhizosphere community. In this study, a microcosm experiment was conducted to investigate the effect of straw-derived biochar on the structural differentiation of SOM and rhizosphere bacterial communities. 13 C NMR spectra showed that the relative abundance of carboxyl, alkyl, N-alkyl, O-alkyl and methoxyl groups decreased by 22%, 31%, 27%, 27% and 27%, respectively, and the relatively stable structure of aryl and O-aryl groups increased by 213% and 41%, respectively. In addition, network-based analysis showed that biochar amendment not only improved the network connectivity of the rhizosphere bacteria, but also enhanced the linkage between bacteria and the molecular structure of SOM. The topological properties of the network, including the number of edges, network density, and average clustering coefficient, were increased by 79%, 15% and 22%, respectively. Moreover, modularization analysis and structural equation model indicated that rhizosphere bacterial network was the important bio-factor affecting the content of labile carbon., (Copyright © 2019 Elsevier B.V. All rights reserved.)

Phytoextraction makes use of trace element-accumulating plants that concentrate the pollutants in their tissues. Pollutants can be then removed by harvesting plants. The success of phytoextraction depends on trace element availability to the roots and the ability of the plant to intercept, take up, and accumulate trace elements in shoots. Current phytoextraction practises either employ hyperaccumulators or fast-growing high biomass plants; the phytoextraction process may be enhanced by soil amendments that increase trace element availability in the soil. This review will focus on the role of plant-associated bacteria to enhance trace element availability in the rhizosphere. We report on the kind of bacteria typically found in association with trace element - tolerating or - accumulating plants and discuss how they can contribute to improve trace element uptake by plants and thus the efficiency and rate of phytoextraction. This enhanced trace element uptake can be attributed to a microbial modification of the absorptive properties of the roots such as increasing the root length and surface area and numbers of root hairs, or by increasing the plant availability of trace elements in the rhizosphere and the subsequent translocation to shoots via beneficial effects on plant growth, trace element complexation and alleviation of phytotoxicity. An analysis of data from literature shows that effects of bacterial inoculation on phytoextraction efficiency are currently inconsistent. Some key processes in plant-bacteria interactions and colonization by inoculated strains still need to be unravelled more in detail to allow full-scale application of bacteria assisted phytoremediation of trace element contaminated soils.