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The emergence of antibiotic-resistant diseases and increases in plant disease outbreaks, that threaten global food security, present major growing public health crises. Since most antibiotics originate from soil microorganisms, soil microbial communities offer promising reservoirs for discovering new compounds. This study explores antibiotic-producing rhizobacteria in Sage Hill's soil, a recently restored environment at UCLA. Biochemical and functional assays were used to characterize soil microbial communities from rhizosphere samples taken from Sage Hill. Using these methods, we identified antibiotic-producing bacteria, and likely Pseudomonas and Bacillus. These results underscore the importance of investigating soil microbial communities for novel antibiotic discovery and agricultural sustainability.

Plants release a wealth of metabolites into the rhizosphere that can shape the composition and activity of microbial communities in response to environmental stress. The connection between rhizodeposition and rhizosphere microbiome succession has been suggested, particularly under environmental stress conditions, yet definitive evidence is scarce. In this study, we investigated the relationship between rhizosphere chemistry, microbiome dynamics, and abiotic stress in the bioenergy crop switchgrass grown in a marginal soil under nutrient-limited, moisture-limited, and nitrogen (N)-replete, phosphorus (P)-replete, and NP-replete conditions. We combined 16S rRNA amplicon sequencing and LC-MS/MS-based metabolomics to link rhizosphere microbial communities and metabolites. We identified significant changes in rhizosphere metabolite profiles in response to abiotic stress and linked them to changes in microbial communities using network analysis. N-limitation amplified the abundance of aromatic acids, pentoses, and their derivatives in the rhizosphere, and their enhanced availability was linked to the abundance of bacterial lineages from Acidobacteria, Verrucomicrobia, Planctomycetes, and Alphaproteobacteria. Conversely, N-amended conditions increased the availability of N-rich rhizosphere compounds, which coincided with proliferation of Actinobacteria. Treatments with contrasting N availability differed greatly in the abundance of potential keystone metabolites; serotonin and ectoine were particularly abundant in N-replete soils, while chlorogenic, cinnamic, and glucuronic acids were enriched in N-limited soils. Serotonin, the keystone metabolite we identified with the largest number of links to microbial taxa, significantly affected root architecture and growth of rhizosphere microorganisms, highlighting its potential to shape microbial community and mediate rhizosphere plant-microbe interactions.

Arsenic contamination of soils threatens the health of millions globally through accumulation in crops. While plants detoxify arsenic via phytochelatin (PC) complexation and efflux of arsenite from roots, arsenite efflux mechanisms are not fully understood. Here, white lupin (Lupinus albus) was grown in semi-hydroponics and exudation of glutathione (GSH) derivatives and PCs in response to arsenic was scrutinised using LC-MS/MS. Inhibiting synthesis of PC precursor GSH with L-buthionine sulfoximine (BSO) or ABC transporters with vanadate drastically reduced (>22%) GSH-derivative and PC2 exudation, but not PC3 exudation. This was accompanied by arsenic hypersensitivity in plants treated with BSO and moderate sensitivity with vanadate treatment. Investigating arsenic-phytochelatin (As-PC) complexation revealed two distinct As-PC complexes, As bound to GSH and PC2 (GS-As-PC2) and As bound to PC3 (As-PC3), in exudates of As-treated lupin. Vanadate inhibited As-PC exudation, while BSO inhibited both the synthesis and exudation of As-PC complexes. These results demonstrate a role of GSH-derivatives and PC exudation in lupin arsenic tolerance and reveal As-PC exudation as a new potential mechanism contributing to active arsenic efflux in plants. Overall, this study uncovers insight into rhizosphere arsenic detoxification with potential to help mitigate pollution and reduce arsenic accumulation in crops.

Soil microbiomes are highly diverse, and to improve their representation in biogeochemical models, microbial genome data can be leveraged to infer key functional traits. By integrating genome-inferred traits into a theory-based hierarchical framework, emergent behaviour arising from interactions of individual traits can be predicted. Here we combine theory-driven predictions of substrate uptake kinetics with a genome-informed trait-based dynamic energy budget model to predict emergent life-history traits and trade-offs in soil bacteria. When applied to a plant microbiome system, the model accurately predicted distinct substrate-acquisition strategies that aligned with observations, uncovering resource-dependent trade-offs between microbial growth rate and efficiency. For instance, inherently slower-growing microorganisms, favoured by organic acid exudation at later plant growth stages, exhibited enhanced carbon use efficiency (yield) without sacrificing growth rate (power). This insight has implications for retaining plant root-derived carbon in soils and highlights the power of data-driven, trait-based approaches for improving microbial representation in biogeochemical models.

The rhizosphere, the soil region influenced by plant roots, represents a dynamic microenvironment where intricate interactions between plants and microorganisms shape soil health, nutrient cycling, and plant growth. Soil microorganisms are integral players in the transformation of materials, the dynamics of energy flows, and the intricate cycles of biogeochemistry. Considerable research has been dedicated to investigating the abundance, diversity, and intricacies of interactions among different microbes, as well as the relationships between plants and microbes present in the rhizosphere. Metagenomics, a powerful suite of techniques, has emerged as a transformative tool for dissecting the genetic repertoire of complex microbial communities inhabiting the rhizosphere. The review systematically navigates through various metagenomic approaches, ranging from shotgun metagenomics, enabling unbiased analysis of entire microbial genomes, to targeted sequencing of the 16S rRNA gene for taxonomic profiling. Each approach's strengths and limitations are critically evaluated, providing researchers with a nuanced understanding of their applicability in different research contexts. A central focus of the review lies in the practical applications of rhizosphere metagenomics in various fields including agriculture. By decoding the genomic content of rhizospheric microbes, researchers gain insights into their functional roles in nutrient acquisition, disease suppression, and overall plant health. The review also addresses the broader implications of metagenomic studies in advancing our understanding of microbial diversity and community dynamics in the rhizosphere. It serves as a comprehensive guide for researchers, agronomists, and policymakers, offering a roadmap for harnessing metagenomic approaches to unlock the full potential of the rhizosphere microbiome in promoting sustainable agriculture. [ABSTRACT FROM AUTHOR]

Capsaicinoids are produced uniquely in pepper fruits, and its level determines the commercial quality and health-promoting properties of pepper. So, it is particularly important to increase capsaicinoids content in pepper. Rhizosphere microbiota is critical to plant growth and performance, and affected by plant varieties. However, the impact of pepper varieties with different capsaicinoids yields on the rhizosphere microbiota is poorly understood. Using high-throughput sequencing of the 16S rRNA and internal transcribed spacer (ITS) region, we investigated the rhizosphere microbial community among five pepper varieties containing different capsaicinoids. Our results demonstrated that pepper variety significantly influenced the diversity and structure of rhizosphere microbial community. Bacterial diversity in varieties with high capsaicinoids content was significantly higher than in varieties with low capsaicinoids content, while fungal diversity was opposite to bacterial diversity. The correlation analysis revealed that 19 dominant bacterial genera (e.g., Chujaibacter, Rhodanobacter, and Gemmatimonas) were significantly correlated with capsaicinoids content, and nine of them were also significantly associated with soil nutrients, whereas only one fungal genus (Podospora) was significantly correlated with capsaicinoids content. Additionally, almost all genera which significantly correlated to capsaicinoids content were biomarkers of the five pepper varieties and the correlation was well corresponding to the capsaicinoids content. Overall, our results confirmed that the variety of pepper significantly affected the rhizosphere microbial community in the fields, and bacteria and fungi responded differently to capsaicinoids, which may affect the biosynthesis of capsaicinoids and contribute to further improvement of capsaicinoids production in pepper fruits. [ABSTRACT FROM AUTHOR]

Introduction: Despite their adverse environmental effects, modern agriculture relies heavily on agrochemicals to manage diseases and pests and enhance plant growth and productivity. Some of these functions could instead be fulfilled by endophytes from the plant microbiota, which have diverse activities beneficial for plant growth and health. Methods: We therefore used a microbiome-guided top-down approach to select ten bacterial strains from different taxa in the core microbiome of tomato plants in the production chain for evaluation as potential bioinoculants. High-quality genomes for each strain were obtained using Oxford Nanopore long-read and Illumina short-read sequencing, enabling the dissection of their genetic makeup to identify phyto-beneficial traits. Results: Bacterial strains included both taxa commonly used as biofertilizers and biocontrol agents (i.e. Pseudomonas and Bacillus) as well as the less studied genera Leclercia, Chryseobacterium, Glutamicibacter, and Paenarthorbacter. When inoculated in the tomato rhizosphere, these strains promoted plant growth and reduced the severity of Fusarium Crown and Root Rot and Bacterial Spot infections. Genome analysis yielded a comprehensive inventory of genes from each strain related to processes including colonization, biofertilization, phytohormones, and plant signaling. Traits directly relevant to fertilization including phosphate solubilization and acquisition of nitrogen and iron were also identified. Moreover, the strains carried several functional genes putatively involved in abiotic stress alleviation and biotic stress management, traits that indirectly foster plant health and growth. Discussion: This study employs a top-down approach to identify new plant growth-promoting rhizobacteria (PGPRs), offering an alternative to the conventional bottom-up strategy. This method goes beyond the traditional screening of the strains and thus can expand the range of potential bioinoculants available for market application, paving the way to the use of new still underexplored genera. [ABSTRACT FROM AUTHOR]

This study aimed for a better understanding of the niche specification of bacteria carrying the tfd-genes for aerobic 2,4-dichlorphenoxyacetic acid (2,4-D) degradation in the rice paddy ecosystem. To achieve this, a dedicated microcosm experiment was set up to mimic the rice paddy system, with and without 2,4-D addition, allowing spatial sampling of the different rice paddy compartments and niches, i.e., the main anaerobic bulk soil and the aerobic surface water, surface soil, root surface and rhizosphere compartments. No effect of 2,4-D on the growth and morphology of the rice plant was noted. 2,4-D removal was faster in the upper soil layers compared to the deeper layers and was more rapid after the second 2,4-D addition compared to the first. Moreover, higher relative abundances of the 2,4-D catabolic gene tfdA and of the mobile genetic elements IncP-1 and IS1071 reported to carry the tfd-genes, were observed in surface water and surface soil when 2,4-D was added. tfdA was also detected in the root surface and rhizosphere compartment but without response to 2,4-D addition. While analysis of the bacterial community composition using high-throughput 16S rRNA gene amplicon sequencing did not reveal expected tfd-carrying taxa, subtle community changes linked with 2,4-D treatment and the presence of the plant were observed. These findings suggest (i) that the surface soil and surface water are the primary and most favorable compartements/niches for tfdmediated aerobic 2,4-D biodegradation and (ii) that the community structure in the 2,4-D treated rice paddy ecosystem is determined by a niche-dependent complex interplay between the effects of the plant and of 2,4-D. [ABSTRACT FROM AUTHOR]

Despite gaining significant attention in recent years, it remains unclear whether mycorrhizal fungi distribute meaningful amounts of resources among trees in ways that increase the fitness of the receiving trees. To investigate this, we used pairs of shaded and unshaded Pinus halepensis or Quercus calliprinos saplings, growing in both inter‐ and intra‐specific combinations outdoors in forest soil. We examined the combined effects of indirect and direct below‐ground connections on tree performance and Non‐Structural Carbohydrate (NSC) pools. Although we did not observe any growth benefits, shaded recipient oaks exhibited higher levels of root and branch NSC compared to their control counterparts, which were not connected below‐ground. This finding suggests a potential benefit of establishing below‐ground connections. However, no such benefits were observed among the unshaded pairs or in the other inter‐ and intra‐specific pairs of pines and oaks. We monitored the carbon (C) flow from a 13CO2‐labelled donor pine tree to a below‐ground connected oak tree and demonstrated C transfer from pines to shaded oaks. We also identified the main fungal symbionts interacting with pines and oaks. Our findings indicate that the effects of below‐ground C transfer are context‐dependent, manifesting in nuanced alterations in plant NSC that are not readily apparent through conventional growth metrics. Read the free Plain Language Summary for this article on the Journal blog. [ABSTRACT FROM AUTHOR]

The "limón sutil" (Citrus aurantifolia) has been widely cultivated and well established for many years in Piura, northwestern Peru, because of its exceptional climate and soil conditions. However, decline and death of C. aurantifolia trees caused by different phytopathogens remain a common problem which has been observed in the last decades. It is known that the microbiota of soil plays an important role with their host and could be the starting point to understand the causes of citrus decline. In this study, we identified through culture-independent methods the bacterial and fungal microbiota associated to C. aurantifolia, C. jambhiri and C. volkameriana rhizospheres in the main areas of Piura. By using a 16S rRNA and ITS-metabarcoding analysis, we evaluated the taxonomic diversity between healthy trees and with decline symptoms and how this diversity could influence the health status of citrus trees. More than 600 and 200 bacterial and fungal ASVs were identified, respectively. Our metabarcoding analysis was able to identify Proteobacteria, Cyanobacteria, Firmicutes, Bacteroidota and Acidobacteriota prokaryotic phyla, while fungal phyla included Ascomycota, Basidiomycota and Glomeromycota. In addition, there were differences between microbial diversity indices in rhizospheres evaluated. Finally, bacterial and fungal genera were shared among the different citrus rhizospheres. These results have allowed us to obtain a preliminary identification of microbiota in the citrus rhizospheres of healthy trees and with decline symptoms. [ABSTRACT FROM AUTHOR]

Moso bamboo is excellent candidate for cadmium (Cd)/lead (Pb) phytoremediation, while rhizosphere microbiome has significant impact on phytoremediation efficiency of host plant. However, little is known about the rhizosphere bacterial communities of moso bamboo in Cd/Pb contaminated soils. Therefore, this study investigated the assembly patterns and key taxa of rhizosphere bacterial communities of moso bamboo in Cd/Pb polluted and unpolluted soils, by field sampling, chemical analysis, and 16S rRNA gene sequencing. The results indicated α-diversity between Cd/Pb polluted and unpolluted soils showed a similar pattern (p > 0.05), while β-diversity was significantly different (p < 0.05). The relative abundance analysis indicated α-proteobacteria (37%) and actinobacteria (31%) were dominant in Cd/Pb polluted soils, while γ-proteobacteria (40%) and α-proteobacteria (22%) were dominant in unpolluted soils. Co-occurrence network analysis indicated microbial networks were less complex and more negative in polluted soils than in unpolluted soils. Mantel analysis indicated soil available phosphorus, organic matter, and available Pb were the most important environmental factors affecting microbial community structure. Correlation analysis showed 11 bacterial genera were significantly positively related to Cd/Pb. Overall, this study identified the bacterial community composition of bamboo rhizosphere in responding to Cd/Pb contamination and provides a theoretical basis for microbe-assistant phytoremediation in the future. Novelty statement: To date, little is known about the bacterial communities in the rhizosphere of moso bamboo under Cd and Pb multiple stresses. This study investigated the assembly patterns and key taxa of rhizospheric bacterial communities of moso bamboo in Cd/Pb polluted and unpolluted soils. It was found that the bacterial community structure in bamboo rhizosphere is easily influenced by soil chemical environment, such as fertilities and heavy metals. The key bacterial taxa identified here could be target microbe in future microbe-assistant phytoremediation. [ABSTRACT FROM AUTHOR]

Despite that climate change is currently one of the most pervasive challenges, its effects on the plant-associated microbiome is still poorly studied. The aim of this study was to evaluate the impact of the independent and combinatory effect of climate warming and drought on the microbiome assembly of oak from seed to seedling. In a multifactorial experimental set up, acorns were subjected to different temperatures (15 °C, 20 °C, and 25 °C) and soil moisture levels (drought (15%) and control (60%)) from germination until the seedling stage, after which the bacterial and fungal communities associated to the rhizosphere and phyllosphere were characterized by amplicon sequencing and qPCR. The results showed a stronger effect of temperature on fungal than on bacterial diversity and the effect was more pronounced in the phyllosphere. Under drought condition, temperature had a significantly negative effect on phyllosphere fungal diversity. In the rhizosphere, temperature had a significant effect on the fungal community composition which was primarily caused by species turnover. Regardless of temperature, Actinobacteriota was significantly enriched in drought, a group of bacteria known to increase plant drought tolerance. This study provides new insights into the effect of climate change on the plant microbiome in natural ecosystems. [ABSTRACT FROM AUTHOR]

Background: Cabbage Fusarium wilt (CFW) is a devastating disease caused by the soil-borne fungus Fusarium oxysporum f. sp. conglutinans (Foc). One of the optimal measures for managing CFW is the employment of tolerant/resistant cabbage varieties. However, the interplay between plant genotypes and the pathogen Foc in shaping the rhizosphere microbial community, and the consequent influence of these microbial assemblages on biological resistance, remains inadequately understood. Results: Based on amplicon metabarcoding data, we observed distinct differences in the fungal alpha diversity index (Shannon index) and beta diversity index (unweighted Bray–Curtis dissimilarity) within the rhizosphere of the YR (resistant to Foc) and ZG (susceptible to Foc) cabbage varieties, irrespective of Foc inoculation. Notably, the Shannon diversity shifts in the resistant YR variety were more pronounced following Foc inoculation. Disease-resistant plant variety demonstrate a higher propensity for harboring beneficial microorganisms, such as Pseudomonas, and exhibit superior capabilities in evading harmful microorganisms, in contrast to their disease-susceptible counterparts. Furthermore, the network analysis was performed on rhizosphere-associated microorganisms, including both bacteria and fungi. The networks of association recovered from YR exhibited greater complexity, robustness, and density, regardless of Foc inoculation. Following Foc infection in the YR rhizosphere, there was a notable increase in the dominant bacterium NA13, which is also a hub taxon in the microbial network. Reintroducing NA13 into the soil significantly improved disease resistance in the susceptible ZG variety, by directly inhibiting Foc and triggering defense mechanisms in the roots. Conclusions: The rhizosphere microbial communities of these two cabbage varieties are markedly distinct, with the introduction of the pathogen eliciting significant alterations in their microbial networks which is correlated with susceptibility or resistance to soil-borne pathogens. Furthermore, we identified a rhizobacteria species that significantly boosts disease resistance in susceptible cabbages. Our results indicated that the induction of resistance genes leading to varied responses in microbial communities to pathogens may partly explain the differing susceptibilities of the cabbage varieties tested to CFW. -meKq2qaHpqpKck3NvZ8m1 Video Abstract [ABSTRACT FROM AUTHOR]

Abstract\nNOVELTY STATEMENTPersistent crude oil contamination poses a significant environmental challenge. In this study, the efficacy of Vigna unguiculata (L.) and associated rhizospheric microorganisms in remediating crude oil-contaminated soil within a microcosm setting was investigated. A randomized block design was employed, and soil samples were subjected to varying degrees of contamination: 0% (UR), 2.5% (CR2), 5.0% (CR5), 7.5% (CR7), and 10.0% (CR10) w/w crude oil. The investigation aimed to assess the potential of Vigna unguiculata (L.) in mitigating crude oil contamination across these defined contamination gradients. The plant growth and crude oil removal were monitored concurrently post-emergence. Plant emergence and growth were significantly affected due to contamination, especially among plants in CR5 and CR10. The bacterial population was higher in the rhizosphere, and the treatments with lower hydrocarbon contamination. It was shown that plant density encouraged the growth of bacterial communities. Significant reduction in soil TPH was observed in CR2 (76.61%) and CR7 (65.88%). There was a strong correlation between plant growth and oil-utilizing bacterial population (r2 = 0.966) and plant growth and hydrocarbon reduction (r2 = 0.956), signifying the role of plant-bacterial synergy. Saturate fractions (C30 – C32) were significantly degraded to lower molecular weight compounds (C11 – C14). Except in CR5 and CR10, the remediation within the cowpea rhizosphere was effective even at regulatory standards. Understanding the rhizosphere ecological dynamics would further highlight the role the bacteria played; hence, it is recommended.The present study established a direct link between bacterial-plant interaction and biodegradation of crude oil. It extensively explored the nature of the degradation and also the fate of the residual oil. The present study achieved high rate of TPH removal within 12 weeks using cowpea alone as against the several previous reports that used other stimulants. [ABSTRACT FROM AUTHOR]

Polygonatum kingianum Collett & Hemsl., is one of the most important traditional Chinese medicines in China. The purpose of this study is to investigate the relationship between herb quality and microbial-soil variables, while also examining the composition and structure of the rhizosphere microbial community in Polygonatum kingianum, the ultimate goal is to provide a scientific approach to enhancing the quality of P. kingianum. Illumina NovaSeq technology unlocks comprehensive genetic variation and biological functionality through high-throughput sequencing. And in this study it was used to analyze the rhizosphere microbial communities in the soils of five P. kingianum planting areas. Conventional techniques were used to measure the organic elements, pH, and organic matter content. The active ingredient content of P. kingianum was identified by High Performance Liquid Chromatography (HPLC) and Colorimetry. A total of 12,715 bacterial and 5487 fungal Operational Taxonomic Units (OTU) were obtained and taxonomically categorized into 81 and 7 different phyla. Proteobacteria, Bacteroidetes, and Acidobacteriae were the dominant bacterial phyla Ascomycota and Basidiomycota were the dominat fungal phyla. The key predictors for bacterial community structure included hydrolysable nitrogen and available potassium, while for altering fungal community structure, soil organic carbon content (OCC), total nitrogen content (TNC), and total potassium content (TPOC) were the main influencing factors. Bryobacter and Candidatus Solibacter may indirectly increase the polysaccharide content of P. kingianum, and can be developed as potential Plant Growth Promoting Rhizobacteria (PGPR). This study has confirmed the differences in the soil and microorganisms of different origins of P. kingianum, and their close association with its active ingredients. And it also broadens the idea of studying the link between plants and microorganisms. [ABSTRACT FROM AUTHOR]

Zinc (Zn) is an essential micronutrient that is found in almost all classes of enzymes. Its deficiency is a well-documented problem among cereal crops that causes decreased crop yields and nutritional quality. Therefore, an experiment was implemented in a randomized block design which included the treatments of bacterial inoculation consisting of T1 (Control), T2 (100% RDF;100:40:20), T3(100% RDF + 25 kg ZnSO4.7 H2O), T4(100%RDF+ ZnSB1– Bacillus sp. strain BAU_A2 @750 ml ha−1), T5 (100%RDF+ ZnSB2– Priestia megaterium strain BAU_A3 @750 ml ha−1), T6 (100%RDF+ ZnSB3-Bacillus subtilis strain BAU_A5@750 ml ha−1). The mineral NPK was applied as per treatments. The results indicated the maximum values of water soluble exchangeable Zn and organically bounded Zn in treatments consisting ZnSB1, ZnSB2 and ZnSB3, respectively. The WS+EXCH-Zn was significantly increased by 68.57%, 28.26%, 18%, 98.14%, 41.30%, 30.00% and 128.12%, 55.55%, 37.25%, 43%, 62.22% and 43.13% in first year (2018–19) and second year (2019–2020) under the soil treated with ZnSB1-Peribacillus simplex strain BAU_A1, ZnSB2-Bacillus sp. strain BAU__A2 and ZnSB3-Bacillus subtilis strain BAU_A5 along with 100%RDF over control, application of recommended dose of fertilizer with and without application of 25 kg ZnSO4 ha−1, respectively. However, the maximum decrement in Mn-oxide-bounded zinc (1.12 mg kg−1 soil) was observed with T6 which was significantly higher by 158%, 194.4%, 185.71% over control, 100% RDF with and without application of 25 kg ZnSO4 ha−1, which showed the solubilization of zinc with the activity of ZnSB in soil. The study may be beneficial to mitigate the zinc deficiency in soil and malnutrition in children. [ABSTRACT FROM AUTHOR]

Manipulating the rhizosphere microbiome to enhance plant stress tolerance is an environmentally friendly technology and a renewable resource to restore degraded environments. Here we suggest a sustainable bioremediation strategy on the example of Stebnyk mine tailings storage. We consider Salicornia europaea rhizosphere community, and the ability of the phytoremediation plant Salix viminalis to recruit its beneficial microbiome to mediate the pollution stress at the Stebnyk mine tailings storage. The tailings contain large amounts of brine salts and heavy metals that contaminate the ground water and surrounding areas, changing soil biogeochemistry and causing increased erosion. The species richness of the endophytic bacterial community of S. viminalis roots was assessed based on observed OTUs, Shannon-InvSimpson, and evenness index. Our results obtained using the plant-based enrichment strategy show that biodiversity was decreased across the contamination zones and that S. europaea supplementation significantly increased the species richness. Our results also indicate that the number of dominating bacteria was not changed across zones in both S. europaea-treated and untreated bacterial populations, and that the decrease in richness was mainly caused by the low abundant bacterial OTUs. The importance of selecting the bioremediation strains that are likely to harbor a reservoir of genetic traits that aid in bioremediation function from the target environment is discussed [ABSTRACT FROM AUTHOR]

Microbial interactions in the rhizosphere contribute to soil health, making understanding these interactions crucial for sustainable agriculture and ecosystem management. Yet it is difficult to understand what we cannot see; among the limitations in rhizosphere imaging are challenges associated with rapidly and noninvasively imaging microbial cells over field depths relevant to plant roots. Here, we present a bimodal imaging technique called complex-field and fluorescence microscopy using the aperture scanning technique (CFAST) that addresses these limitations. CFAST integrates quantitative phase imaging using synthetic aperture imaging based on Kramers-Kronig relations, along with three-dimensional (3D) fluorescence imaging using an engineered point spread function. We showcase CFAST's practicality and versatility in two ways. First, by harnessing its depth of field of more than 100 µm, we significantly reduce the number of captures required for 3D imaging of plant roots and bacteria in the rhizoplane. This minimizes potential photobleaching and phototoxicity issues. Second, by leveraging CFAST's phase sensitivity and fluorescence specificity, we track microbial growth, competition, and gene expression at early stages of colony biofilm development. Specifically, we resolve bacterial growth dynamics of mixed populations without the need for genetically labeling environmental isolates. Moreover, we find that gene expression related to phosphorus sensing and antibiotic production varies spatiotemporally within microbial populations that are surface attached and appears distinct from their expression in planktonic cultures. Together, CFAST's attributes overcome commercial imaging platform limitations and enable insights to be gained into microbial behavioral dynamics in experimental systems of relevance to the rhizosphere. [ABSTRACT FROM AUTHOR]

Modern agriculture's goal of improving crop resource acquisition efficiency relies on the intricate relationship between the root system and the soil. Root and rhizosphere traits play a critical role in the efficient use of nutrients and water, especially under dynamic environments. This review emphasizes a holistic perspective, challenging the conventional separation of nutrient and water uptake processes and the necessity for an integrated approach. Anticipating climate change-induced increase in the likelihood of extreme weather events that result in fluctuations in soil moisture and nutrient availability, the study explores the adaptive potential of root and rhizosphere traits to mitigate stress. We emphasize the significance of root and rhizosphere characteristics that enable crops to rapidly respond to varying resource availabilities (i.e. the presence of water and mobile nutrients in the root zone) and their accessibility (i.e. the possibility to transport resources to the root surface). These traits encompass for example root hairs, mucilage and extracellular polymeric substance (EPS) exudation, rhizosheath formation and the expression of nutrient and water transporters. Moreover, we recognize the challenge of balancing carbon investments, especially under stress, where optimized traits must consider carbon-efficient strategies. To advance our understanding, the review calls for well-designed field experiments, recognizing the limitations of controlled environments. Non-destructive methods such as mini rhizotron assessments and in-situ stable isotope techniques, in combination with destructive approaches such as root exudation analysis, are proposed for assessing root and rhizosphere traits. The integration of modeling, experimentation, and plant breeding is essential for developing resilient crop genotypes capable of adapting to evolving resource limitation. [ABSTRACT FROM AUTHOR]

To elucidate the biological mechanisms driving the growth of various pumpkin varieties to different sizes under identical management conditions while in the same field, the soil microbial community structures in the rhizospheres of giant-pumpkin (GP) and small-pumpkin (SP) varieties were analyzed. The results revealed that a significantly higher abundance of bacterial communities could be detected in the rhizospheres of the giant pumpkin varieties, such as Gemmatimonadota, norank__f__norank__o_Gaiellales, norank__f__Gemmatimonadaceae, Bryobacter, Sphingomonas, norank__f__JG30-KF-AS9, and norank__f__norank__o___Elsterales, than in those of the small-sized pumpkins. Additionally, norank_f__norank_o__Elsterale, Ellin6067, norank_f__67-14, and Chujaibacter were unique dominant soil bacteria genera in the rhizospheres of the giant pumpkins. By contrast, Arthrobacter, norank_f__Roseiflexaceae, unclassified_f__Rhizobiaceae, Allorhizobium-Neorhizobium-Pararhizobium-Rhizobium, Nocardioides, Mycobacterium, norank_f__norank_o__Vicinamibacterales, and Burkholderia-Caballeronia-Paraburkholderia were the unique dominant soil bacterial genera in the rhizospheres of the small pumpkins. Moreover, at the fungal genus level, unclassified_c__Chytridiomycetes, Podosphaera, and Colletotrichum presented significant differences between the giant-pumpkin (GP) and small-pumpkin (SP) rhizospheres. In addition, unclassified__p__Rozellomycota, unclassified__c__Chytridiomycetes, Penicillium, and unclassified__f__Chaetomiaceae were unique dominant soil fungal genera in the rhizospheres of the giant pumpkins (GPs). By contrast, Podosphaera, Colletotrichum, unclassified__f__Plectosphaerellaceae, unclassified__o_Boletales, Scytalidium, unclassified__p__Rozellomycota, and unclassified__o_Agaricales were the unique dominant soil fungal genera in the rhizospheres of the small pumpkins (SPs). PICRUSt and FUNGuild functional prediction analyses revealed that the giant-pumpkin rhizosphere microbial community had significantly increased translation, ribosomal structure and biogenesis, nucleotide transport and metabolism, defense mechanisms, replication, recombination and repair, wood saprotroph, and undefined saprotroph levels. The above results suggest that the soil microbial compositions differed between the rhizospheres of the giant- (GP) and small-pumpkin (SP) varieties, even though the plants were grown in the same field under identical management conditions. Meanwhile, bacterial genera such as norank_f__norank_o__Elsterale, Ellin6067, norank_f__67-14, and Chujaibacter, in addition to fungal genera such as unclassified__p__Rozellomycota, unclassified__c__Chytridiomycetes, Penicillium, and unclassified__f__Chaetomiaceae, can be speculated as potential soil functional micro-organisms associated with improved pumpkin size. [ABSTRACT FROM AUTHOR]

To explore and utilize the abundant soil microorganisms and their beneficial functions, high-throughput sequencing technology was used to analyze soil microbial compositions in the rhizosphere of red and green amaranth varieties. The results showed that significant differences in soil microbial composition could be found in the rhizosphere of amaranth plants with different color phenotypes. Firstly, soil bacterial compositions in the rhizosphere were significantly different between red and green amaranths. Among them, Streptomyces, Pseudonocardia, Pseudolabrys, Acidibacter, norank_ f_ Micropepsaceae, Bradyrhizobium, and Nocardioides were the unique dominant soil bacterial genera in the rhizosphere of red amaranth. In contrast, Conexibacter, norank_f_norank_o_norank_c_TK10, and norank_f_ norank_o_ norank_ c_AD3 were the special dominant soil bacterial genera in the rhizosphere of green amaranth. Additionally, even though the soil fungal compositions in the rhizosphere were not significantly different between red and green amaranths, the abundance of the dominant soil fungal genera in the rhizosphere showed significant differences between red and green amaranths. For example, unclassified_k__Fungi, Fusarium, Cladophialophora, unclassified_c__Sordariomycetes and unclassified_p__Chytridiomycota significantly enriched as the dominant soil fungal genera in the rhizosphere of the red amaranth. In contrast, Aspergillues only significantly enriched as the dominant soil fungal genus in the rhizosphere of green amaranth. All of the above results indicated that amaranth with various color phenotypes exactly recruited different microorganisms in rhizosphere, and the enrichments of soil microorganisms in the rhizosphere could be speculated in contributing to amaranth color formations. [ABSTRACT FROM AUTHOR]

Introduction: Rhizosphere effects (REs) have recently been identified as important regulators of root and microbial nutrient acquisition and are positively involved in nutrient cycling of belowground carbon (C), nitrogen (N), and phosphorus (P). Nutrient conditions of the fine roots and soil N are likely to influence REs. Still, it is unclear how REs of soil nutrients themselves variably impact the supply of nutrients to plants in terms of the responses to soil N due to succession. Methods: In this study, we applied both fine roots and extracellular enzymes for vector analysis and stoichiometry of N:P to explore the metabolic limitations of roots and rhizospheric soil microbes and their relationships with REs across five levels of soil N (0, 5, 10, 15, and 20 kg N m-2 year-1) along successional age classes of 42, 55, and 65 years in a Pinus tabuliformis forest. Results: Overall, the metabolism of root and rhizospheric soil microbes was mediated by soil N. N limitation of roots initially decreased before increasing, whereas that of microbes demonstrated opposite trends to the N levels owing to competition for inorganic N between them by REs of NO3--N. However, N limitations of both roots and microbes were alleviated in young stands and increased with succession after the application of N. In addition, root N limitations were manipulated by REs of three different soil N-related indicators, i.e., total N, NH4 +-N, and NO3 --N. Rhizospheric soil microbial N limitation was almost unaffected by REs due to their strong homeostasis but was an important driver in the regulation of root N limitation. Discussion: Our results indicated that successional age was the most critical driver that directly and indirectly affected root N metabolism. However, the level of N application had a slight effect on root N limitation. Microbial N limitation and variations in the REs of N indicators regulated root N limitation in the rhizosphere. As a result, roots utilized REs to sequester N to alleviate N limitations. These findings contribute to novel mechanistic perspectives on the sustainability of N nutrition by regulating N cycling in a system of plant-soil-microbes in the rhizosphere to adapt to global N deposition or the heterogeneous distribution of bioavailable soil N with succession. [ABSTRACT FROM AUTHOR]

Tree lines in high latitudes and high altitudes are considered sentinels of global change. This manifests in accelerated encroachment of trees and shrubs and enhanced plant productivity, with currently unknown implications for the carbon balance of these biomes. Given the large soil organic carbon stocks in many tree line soils, we here wondered whether introducing highly productive plants would accelerate carbon cycling through rhizosphere priming effects and if certain soils would be more vulnerable to carbon loss from positive priming than others. To test this, organic and mineral soils were sampled above and below tree lines in the Swedish sub‐arctic and the Peruvian Andes. A greenhouse experiment was then performed to quantify plant‐induced changes in soil mineralisation rates (rhizosphere priming effect) and new C formation using natural abundance labelling and the C4‐species Cynodon dactylon. Several environmental, plant, soil and microbial parameter were monitored during the experiment to complement the observations on soil C cycling. Priming was predominantly positive at the beginning of the experiment, then systematically decreased in all soils during the plant growth season to be mostly negative at the end of the experiment at plant senescence. Independent of direction of priming, the magnitude of priming was always greater in organic than in corresponding mineral soils, which was best explained by the higher C contents of these soils. Integrated over the entire study period, the overall impact of priming (positive and negative) on the soil C balance was mostly negligible. Though net soil C loss was observed in organic soils from the sub‐arctic tundra in Sweden. Most notably, positive and negative priming effects were not mutually exclusive, rather omnipresent across ecosystems, depending on sampling time. The direction of priming seems to be fluctuating with plant productivity, rhizosphere carbon inputs and nutrient uptake. This highlights the need for integrative long‐term studies if we aim to understand priming effects at ecosystem scale and greenhouse and laboratory studies must be validated in situ to enable reliable ecological upscaling. Read the free Plain Language Summary for this article on the Journal blog. [ABSTRACT FROM AUTHOR]

The colonization of alien plants in new habitats is typically facilitated by microorganisms present in the soil environment. However, the diversity and structure of the archaeal, bacterial, and fungal communities in the latitudinal spread of alien plants remain unclear. In this study, the rhizosphere and bulk soil of Chromolaena odorata were collected from five latitudes in Pu' er city, Yunnan Province, followed by amplicon sequencing of the soil archaeal, bacterial, and fungal communities. Alpha and beta diversity results revealed that the richness indices and the structures of the archaeal, bacterial, and fungal communities significantly differed along the latitudinal gradient. Additionally, significant differences were observed in the bacterial Shannon index, as well as in the structures of the bacterial and fungal communities between the rhizosphere and bulk soils. Due to the small spatial scale, trends of latitudinal variation in the archaeal, bacterial, and fungal communities were not pronounced. Total potassium, total phosphorus, available nitrogen, available potassium and total nitrogen were the important driving factors affecting the soil microbial community structure. Compared with those in bulk soil, co-occurrence networks in rhizosphere microbial networks presented lower complexity but greater modularity and positive connections. Among the main functional fungi, arbuscular mycorrhizae and soil saprotrophs were more abundant in the bulk soil. The significant differences in the soil microbes between rhizosphere and bulk soils further underscore the impact of C. odorata invasion on soil environments. The significant differences in the soil microbiota along latitudinal gradients, along with specific driving factors, demonstrate distinct nutrient preferences among archaea, bacteria, and fungi and indicate complex microbial responses to soil nutrient elements following the invasion of C. odorata. [ABSTRACT FROM AUTHOR]

Canada thistle is a pervasive perennial weed, causing challenges to agricultural and natural ecosystems globally. Although research has focused on the phenology, genetics, and control of Canada thistle, little is known about the rhizosphere microbiome and the role plant–microbe interactions play in invasion success. This study investigated the rhizosphere microbiome of Canada thistle across diverse climates, soils, and crops in the U.S. northern Great Plains. Soil and rhizosphere samples were collected and bacterial 16S and fungal ITS2 sequencing were performed to characterize the core microbiome and identify potential factors contributing to invasion success. Amplicon sequencing revealed a stable core microbiome that was detected in the Canada thistle rhizosphere across all locations. The core microbiome was dominated by the bacterial phyla Actinobacteriota and Proteobacteria and fungal phyla Ascomycota and Basidiomycota. Differential abundance analysis showed rhizosphere fungal communities were enriched in pathogen-containing genera with a 1.7-fold greater abundance of Fusaria and a 2.6-fold greater abundance of Gibberella compared to bulk soil. Predictive functional profiling showed rhizosphere communities were enriched (p < 0.05, FDR corrected) in plant pathogen fungal guilds which represented 19% of the fungal community. The rhizosphere microbiome was similar in composition across environments, highlighting the stable association between Canada thistle and specific microbial taxa. This study characterized the core microbiome of Canada thistle, and the findings highlight plant–microbe interactions shaping invasive behavior. These findings are important for understanding the ecological impacts of plant invasion and soil-microbe ecological processes. [ABSTRACT FROM AUTHOR]

Some plant-associated microorganisms could improve host plants biotic and abiotic stress tolerance. Imperata cylindrica is a dominant pioneer plant in some abandoned mine lands with higher concentrations of heavy metal (HM). To discover the specific microbiome of I. cylindrica in this extreme environment and evaluate its role, the microbiome of I. cylindrica’s seeds and rhizosphere soils from HM heavily contaminated (H) and lightly contaminated (L) sites were studied. It was found that HM-contamination significantly reduced the richness of endophytic bacteria in seeds, but increased the abundance of resistant species, such as Massilia sp. and Duganella sp. Spearman’s rank correlation coefficient analysis showed that both Massilia sp. and Duganella sp. showed a significant positive correlation with Zn concentration, indicating that it may have a strong tolerance to Zn. A comparison of the microbiome of rhizosphere soils (RS) and adjacent bare soils (BS) of site H showed that I. cylindrica colonization significantly increased the diversity of fungi in rhizosphere soil and the abundance of Ascomycota associated with soil nutrient cycling. Spearman’s rank correlation coefficient analysis showed that Ascomycota was positively correlated with the total nitrogen. Combined with the fact that the total nitrogen content of RS was significantly higher than that of BS, we suppose that Ascomycota may enhance the nitrogen fixation of I. cylindrica, thereby promoting its growth in such an extreme environment. In conclusion, the concentration of HM and nutrient contents in the soil significantly affected the microbial community of rhizosphere soils and seeds of I. cylindrica, in turn, the different microbiomes further affected soil HM concentration and nutrient contents. The survival of I. cylindrica in HM severely contaminated environment may mainly be through recruiting more microorganisms that can enhance its nutrition supply. [ABSTRACT FROM AUTHOR]

The taxonomic composition of soil (Technosol and Retisol) bacterial communities near the salt dump of a potassium enterprise (Solikamsk, Perm krai) was analyzed by the method of high-throughput sequencing of the 16S rRNA gene. Soil samples without plants and of the rhizosphere of plants of the species Calamagrostis epigeios (L.) Roth from plots located 1–1.5, 8, and 780 m and 11 km from the salt dump were studied. It was found that bacteria of the phyla Pseudomonadota, Bacteroidota, Actinomycetota, Acidobacteriota, Verrucomicrobiota, and Gemmatimonadota predominated in all soil samples. The impact of halite waste on the taxonomic composition of bacterial communities in soils was the greatest on plots in the salinization zone in the immediate vicinity of the salt dump (1–1.5 m). In soil samples without plants taken in these areas, bacteria of the order "Candidatus Actinomarinales" predominated, the proportion of representatives of the phyla Acidobacteriota and Verrucomicrobiota, the class Actinobacteria, and the family Chitinophagaceae decreased, and the proportion of bacteria of the family Xanthomonadaceae in bacterial communities increased in comparison with nonsaline soils (at a distance of 8 and 780 m and 11 km from the salt dump). In the rhizosphere bacterial communities of plants, growing in the salinization zone, the proportion of representatives of the phylum Acidobacteriota and of the families Chitinophagaceae and Enterobacteriaceae decreased, while the proportion of the families Xanthomonadaceae and Flavobacteriaceae became greater. The influence of the salt dump on soil bacterial communities from plots located 8 m and 730 m from the salt dump was revealed: it was manifested in the presence of representatives of the order "Candidatus Actinomarinales" (1.4–1.6%), of the families Nitrosomonadaceae (3.0–6.1%) and Saprospiraceae (1.0–1.9%), of the genus Ilumatobacter (1.6–2.8%), and of nonculturable bacteria of the family Rhodanobacteraceae (1.3–1.5%). [ABSTRACT FROM AUTHOR]

Previously it was shown that endophytic bacteria had the ability to move out of the roots of pea plant seedlings (Pisum sativum L.) into the rhizosphere. In this study, six distinct bacterial strains were isolated from the root growth medium during the cultivation of seedlings in an aqueous medium. By analyzing the nucleotide sequence of 16S rRNA genes, the taxonomic position of these strains was established. Their morphological and cultural parameters were assessed, and the activity of hydrolytic enzymes (pectinase, cellulase, protease) and the IAA-producing capability were examined. It has been observed that the quantity of endophytic bacteria that appears on the root surface during the growth of pea seedlings significantly surpasses the quantity present in the root tissues. It is assumed that hydrolytic enzymes such as pectinase and cellulase are involved in the release of bacteria into the external environment, causing the destruction of carbohydrate structures in plant cell walls. The metabolic parameters established in the studied strains, and the significance of these endophytic bacteria for the host plant after their exit from the roots into the rhizosphere are under discussion. [ABSTRACT FROM AUTHOR]

Background and aims: The differences in multi-elemental concentrations among plant species provide insightful information for understanding species coexistence in forest ecosystems, known as the biogeochemical niche separation. As most of the studies focused on leaf elemental concentrations, it is unclear whether belowground fine roots exhibit biogeochemical niche separation and whether there are close linkages of elemental concentrations among leaves, fine roots and rhizosphere soils. Methods: Nine element (N, P, K, Ca, Mg, Mn, Zn, Cu, and Fe) concentrations in leaves, fine roots and rhizosphere soils were measured for three tree species, three woody shrub species, and three herbaceous species in three subtropical plantations. Results: Elemental concentrations in leaves and fine roots were significantly different between woody and herbaceous species. Notably, the elemental concentrations differed more significantly for leaves than for fine roots, which indicated that leaves, as the most metabolically active tissues, tended to maintain their unique elemental concentrations within a particular functional type. Despite the different elemental needs between leaves and fine roots, most elemental concentrations of leaves were closely associated with those of the fine roots, highlighting the relationship between leaf and root ecological processes. Elemental concentrations in leaves or fine roots were not significantly correlated with those of the rhizospheres. Conclusions: There is evidence for biogeochemical niche separation between coexisting woody and herbaceous species to avoid competition. Our results generalized the biogeochemical niche hypothesis to belowground tissues, which offered new insights into a better understanding of species evolution and coexistence in ecosystems. [ABSTRACT FROM AUTHOR]

Drought is one of the major yield‐limiting factors under climatic adversaries. The positive role of silicon (Si) in drought tolerance of plants has unfolded a new avenue for enhancing crop productivity through better Si use efficiency. It is hence interesting to understand the mechanistic insights pertaining to its beneficial roles under drought stress conditions. Higher plants sense drought stress via roots which, regulate aboveground plant growth under stress. Cellular and molecular modulations occurring at the root and soil interphases influence the survival and growth of plants under drought stress; therefore, it is intriguing to know how Si influences the soil–root interphase and how this interaction augments overall plant growth under drought. In this review, we summarised the roles of Si in the root systems, rhizosphere and their interactions that could improve plant's growth and development under drought conditions. We have discussed the direct and indirect effects of Si‐induced belowground changes on plant roots, soil physical, chemical and biological properties, and their mutual interactions in eliciting defence signalling, including hormone signalling pathways. A mechanistic model of Si‐induced beneficial effects in water‐limited environments is suggested, which could help improve the management of rainfed croplands through Si fertilisation. [ABSTRACT FROM AUTHOR]

Rhizosphere microbial communities play a substantial role in plant productivity. We studied the rhizosphere bacteria and fungi of 51 distinct potato cultivars grown under similar greenhouse conditions using a metabarcoding approach. As expected, individual cultivars were the most important determining factor of the rhizosphere microbial composition; however, differences were also obtained when grouping cultivars according to their growth characteristics. We showed that plant growth characteristics were related to deterministic and stochastic assembly processes of bacterial and fungal communities, respectively. The bacterial genera Arthrobacter and Massilia (known to produce indole acetic acid and siderophores) exhibited greater relative abundance in high- and medium-performing cultivars. Bacterial co-occurrence networks were larger in the rhizosphere of these cultivars and were characterized by a distinctive combination of plant beneficial Proteobacteria and Actinobacteria along with a module of diazotrophs namely Azospira, Azoarcus , and Azohydromonas. Conversely, the network within low-performing cultivars revealed the lowest nodes, hub taxa, edges density, robustness, and the highest average path length resulting in reduced microbial associations, which may potentially limit their effectiveness in promoting plant growth. Our findings established a clear pattern between plant productivity and the rhizosphere microbiome composition and structure for the investigated potato cultivars, offering insights for future management practices. [ABSTRACT FROM AUTHOR]

Here we review the 400-year history of hydroponic culture and describe a unique management approach that does not require leaching or discarding solution between harvests. Nutrients are maintained at a low and steady concentration by daily additions of a dilute solution that replaces the transpired water along with the nutrients that were removed in growth each day. A stable pH and a low steady-state concentration of ammonium are maintained through automated additions of a solution of nitric acid and ammonium nitrate. Ample solution volume (at least 20 cm deep) stabilizes nutrient concentrations, reduces root density, and improves uniformity. Gentle aeration at ≈100 mL·min-1·L-1 maintains dissolved oxygen near saturation and increases uniformity throughout the rhizosphere. These practices facilitate a uniform, closed, root zone with rigorous pH control that provides the micromolar nutrient concentrations of N and P that are representative of field soils. [ABSTRACT FROM AUTHOR]

The intensive applications of nanomaterials in the agroecosystem led to the creation of several environmental problems. More efforts are needed to discover new insights in the nanomaterial–microbe–plant nexus. This relationship has several dimensions, which may include the transport of nanomaterials to different plant organs, the nanotoxicity to soil microbes and plants, and different possible regulations. This review focuses on the challenges and prospects of the nanomaterial–microbe–plant nexus under agroecosystem conditions. The previous nano-forms were selected in this study because of the rare, published articles on such nanomaterials. Under the study's nexus, more insights on the carbon nanodot–microbe–plant nexus were discussed along with the role of the new frontier in nano-tellurium–microbe nexus. Transport of nanomaterials to different plant organs under possible applications, and translocation of these nanoparticles besides their expected nanotoxicity to soil microbes will be also reported in the current study. Nanotoxicity to soil microbes and plants was investigated by taking account of morpho-physiological, molecular, and biochemical concerns. This study highlights the regulations of nanotoxicity with a focus on risk and challenges at the ecological level and their risks to human health, along with the scientific and organizational levels. This study opens many windows in such studies nexus which are needed in the near future. [ABSTRACT FROM AUTHOR]

It is unclear how elevated CO2 (eCO2) and warming interactively influence soil N mineralization in the rhizosphere of rice (Oryza sativa L.), given that the N mineralization process in anaerobic paddy soils differs from that of aerobic upland soils. In this study, we conducted a rhizobox experiment in open top chambers and used 15N-13C dual-labeling to examine the impacts of eCO2 (700 ppm) and warming (2 °C above the ambient) on N mineralization and associated microbial processes in the rhizosphere of rice plants under anaerobic conditions. Compared to the control, the combination of eCO2 and warming increased rice N uptake by 50% in a no-added-N treatment and 32% under an N-added treatment, with the additional uptake mainly consisting of soil-derived N. Co-elevation of CO2 and temperature increased microbial biomass C and N and increased N mineralization by 41% and 23% in the no-added-N and N-added treatments, respectively. The absolute abundances of the N-mineralization genes chiA, pepA, pepN, and urea hydrolysis gene ureC in the rhizosphere increased by 22–30% under eCO2 and warming, corresponding to the additional N mineralization and photosynthetic C allocation into the soil. However, eCO2 plus warming did not increase the metabolic efficiency of N mineralization (mineralized N per unit microbial N). Our results suggest that the co-elevation of CO2 and temperature stimulated microbially mediated soil N mineralization in the rhizosphere of rice, posing a risk on the acceleration of soil organic matter decomposition. [ABSTRACT FROM AUTHOR]

Background: Peanut (Arachis hypogaea L.) is regarded as a crop with high nutrient use efficiency, but there may be differences between cultivars. Furthermore, there is little information on the strategy of peanut cultivars to adapt to soil P availability and to what extent they explore non‐labile P pools. Aims: Our objective was to evaluate growth, root morphology, enzymatic activity in the rhizosphere, and P uptake of peanut cultivars grown under different soil P status. Methods: The study was conducted in a greenhouse in 6‐L pots. Soils with low P (without fertilization) and high P content (with fertilization) and seven peanut cultivars of different origins, different maturation groups, and release years were investigated. Peanut shoot yield, phosphorus uptake, root growth, soil P fractions as well as phosphatase activity in the rhizosphere soil were determined. Results: In P‐deficient soil, a higher dry matter yield was associated with longer root hairs and root length, which resulted in decreased soil non‐labile P was observed mainly with cultivars developed in Argentina (ARG‐medium‐old and ARG‐medium‐new) and the late maturity Brazilian cultivar (BR I‐late new). These cultivars adapted well to P deficiency and were less dependent on labile P. New Brazilian early and medium maturity cultivars developed less, shorter root hairs, and showed low acid phosphatase activity in the rhizosphere under P deficiency, resulting in lower P uptake and dry matter yield. Under high P availability, new Brazilian cultivars of medium and late maturity showed the highest dry matter yield (9.0 and 9.8 g plant−1, respectively) and longest roots, around 120 m plant−1. High P availability decreased root hairs in all cultivars. Conclusion: Overall, the adaptation of peanut cultivars to P‐deficient soils was lower for the new mid‐ and early‐maturing Brazilian cultivars compared with the Argentinian and old or late‐maturing Brazilian cultivars. The main strategies of P‐efficient cultivars under low P availability are to increase root length, root hair length, and root hair density. [ABSTRACT FROM AUTHOR]

Summary The onset of stomatal closure reduces transpiration during drought. In seed plants, drought causes declines in plant water status which increases leaf endogenous abscisic acid (ABA) levels required for stomatal closure. There are multiple possible points of increased belowground resistance in the soil–plant atmospheric continuum that could decrease leaf water potential enough to trigger ABA production and the subsequent decreases in transpiration. We investigate the dynamic patterns of leaf ABA levels, plant hydraulic conductance and the point of failure in the soil–plant conductance in the highly embolism‐resistant species Callitris tuberculata using continuous dendrometer measurements of leaf water potential during drought. We show that decreases in transpiration and ABA biosynthesis begin before any permanent decreases in predawn water potential, collapse in soil–plant hydraulic pathway and xylem embolism spread. We find that a dynamic but recoverable increases in hydraulic resistance in the soil in close proximity to the roots is the most likely driver of declines in midday leaf water potential needed for ABA biosynthesis and the onset of decreases in transpiration. [ABSTRACT FROM AUTHOR]

Plants rhizosphere and bacterial communities' association offer great advantages for its adaptation to adverse conditions in desert ecosystems. In the Sonoran Desert, Mexico, there is low diversity of species due to the significant incidence of high salinity, drought and extreme temperatures. However, Parkinsonia aculeata L. is an endemic species adapted to these adverse environmental conditions. Here, we aimed to isolate and molecularly characterize bacterial isolates associated with P. aculeata rhizosphere grown in saline soils (BL site) and drought (RT site). A total of thirty-three bacteria isolates from the P. aculeata rhizosphere were identified by 16S rDNA sequencing finding members of the genera: Bacillus, Enterobacter, Priestia, Sinomonas, Micrococcus, Kocuria, Staphylococcus, Streptomyces, Arthrobacter and Peribacillus. Priestia followed by Bacillus and Staphylococcus genus showed the major abundance percentages in both sites. The isolated strains were previously reported to exhibit plant beneficial traits, promote plant growth preserve the soil, provide an opportunity for the development of environmentally friendly alternatives for agriculture and to be used as experimental models to study drought/salt mitigation. [ABSTRACT FROM AUTHOR]

Tree‐mycorrhizal associations are associated with patterns in nitrogen (N) availability and soil organic matter storage; however, we still lack a mechanistic understanding of what tree and fungal traits drive these patterns and how they will respond to global changes in soil N availability. To address this knowledge gap, we investigated how arbuscular mycorrhizal (AM)‐ and ectomycorrhizal (EcM)‐associated seedlings alter rhizodeposition in response to increased seedling inorganic N acquisition. We grew four species each of EcM and AM seedlings from forests of the eastern United States in a continuously 13C‐labeled atmosphere within an environmentally controlled chamber and subjected to three levels of 15N‐labeled fertilizer. We traced seedling 15N uptake from, and 13C‐labeled inputs (net rhizodeposition) into, root‐excluded or ‐included soil over a 5‐month growing season. N uptake by seedlings was positively related to rhizodeposition for EcM‐ but not AM‐associated seedlings in root‐included soils. Despite this contrast in rhizodeposition, there was no difference in soil C storage between mycorrhizal types over the course of the experiment. Instead root‐inclusive soils lost C, while root‐exclusive soils gained C. Our findings suggest that mycorrhizal associations mediate tree belowground C investment in response to inorganic N availability, but these differences do not affect C storage. Continued soil warming and N deposition under global change will increase soil inorganic N availability and our seedling results indicate this could lead to greater belowground C investment by EcM‐associated trees. This potential for less efficient N uptake by EcM‐trees could contribute to AM‐tree success and a shift toward more AM‐dominated temperate forests. [ABSTRACT FROM AUTHOR]

Background: Elucidating the intricate structural organization and spatial gradients of biomolecular composition within the rhizosphere is critical to understanding important biogeochemical processes, which include the mechanisms of root-microbe interactions for maintaining sustainable plant ecosystem services. While various analytical methods have been developed to assess the spatial heterogeneity within the rhizosphere, a comprehensive view of the fine distribution of metabolites within the root-soil interface has remained a significant challenge. This is primarily due to the difficulty of maintaining the original spatial organization during sample preparation without compromising its molecular content. Results: In this study, we present a novel approach, RhizoMAP, in which the rhizosphere molecules are imprinted on selected polymer membranes and then spatially profiled using matrix-assisted laser desorption/ionization (MALDI) mass spectrometry imaging (MSI). We enhanced the performance of RhizoMAP by combining the use of two thin (< 20 μm) membranes (polyester and polycarbonate) with distinct MALDI sample preparations. This optimization allowed us to gain insight into the distribution of over 500 different molecules within the rhizosphere of poplar (Populus trichocarpa) grown in rhizoboxes filled with mycorrhizae soil. These two membranes, coupled with three different sample preparation conditions, enabled us to capture the distribution of a wide variety of molecules that included phytohormones, amino acids, sugars, sugar glycosides, polycarboxylic acids components of the Krebs cycle, fatty acids, short aldehydes and ketones, terpenes, volatile organic compounds, fertilizers from the soil, and others. Their spatial distribution varies greatly, with some following root traces, others showing diffusion from roots, some associated with soil particles, and many having distinct hot spots along the plant root or surrounding soil. Moreover, we showed how RhizoMAP can be used to localize the origin of the molecules and molecular transformation during root growth. Finally, we demonstrated the power of RhizoMAP to capture molecular distributions of key metabolites throughout a 20 cm deep rhizosphere. Conclusions: RhizoMAP is a method that provides nondestructive, untargeted, broad, and sensitive metabolite imaging of root-associated molecules, exudates, and soil organic matter throughout the rhizosphere, as demonstrated in a lab-controlled native soil environment. [ABSTRACT FROM AUTHOR]

Water is vital for all living rhizospheric organisms. However, numerous microorganisms have adapted to survive in environments in which water is scarce. Recent evidence has indicated that sugars from root or microbial source is linked with water deficit tolerance of crops. Here we described in olive trees the changes in sugars accumulation in roots, in combination with corresponding changes in microbial and soluble sugar profiles in the rhizosphere under drought conditions. A marked increase in mannitol content occurred in roots of water-stressed plants. Application of drought stress caused a significant increase in the level of microbial trehalose when compared to the control. Trehalose may increase the soil water surface tension, which could facilitate drought tolerance of olive. We showed that complex interactions of root and microbial community in the rhizosphere maintained the relative water content at 60 % under drought conditions and have the potential to regulate the water uptake by olive. [Display omitted] • The main sugar compound in water-stressed olive roots was mannitol. • The main microbial sugar in water-stressed olive rhizosphere was trehalose. • Thus trehalose may be used as a specific indicator of microbial drought tolerance. [ABSTRACT FROM AUTHOR]

Grasslands are the predominant land use type in China, which is currently encountering significant desertification issues. Consequently, restoring grassland vegetation has important implications for terrestrial carbon (C) levels and, consequently, the global C balance. This study focused on Salix cupularis, the primary plant used for desert control on the eastern edge of the Qinghai-Tibet Plateau. We analysed the rhizosphere and non-rhizosphere soil up to the depth of 60 cm after Salix cupularis growth for 0–24 years, examining soil total organic carbon (TOC) and its labile fractions. Following restoration, there was a gradual increase in TOC and its labile fractions, with the most significant changes observed in the rhizosphere soil at a depth of 0–20 cm. After 24 years of restoration, the TOC content in both rhizosphere and non-rhizosphere soil had increased by 141.74% and 39.44%, respectively. Labile organic C in the rhizosphere soil increased more rapidly and pronouncedly compared with the TOC. Specifically, dissolved organic C and easily oxidised organic C in the rhizosphere soil saw substantial increases of 211.03% and 217.65%, respectively. Meanwhile, compared with the 4 years of restoration, soil C pool management index of the 8–24 years soils increased, ranging from 15.70% to 132.21%. Therefore, long-term vegetation restoration on the eastern margin of the Qinghai-Tibet Plateau can significantly enhance TOC and its labile fractions, as well as improve soil C sink capacity and quality. [ABSTRACT FROM AUTHOR]

Methanotrophs of the genus Methylocystis are frequently found in rice paddies. Although more than ten facultative methanotrophs have been reported since 2005, none of these strains was isolated from paddy soil. Here, a facultative methane-oxidizing bacterium, Methylocystis iwaonis SD4, was isolated and characterized from rhizosphere samples of rice plants in Nanjing, China. This strain grew well on methane or methanol but was able to grow slowly using acetate or ethanol. Moreover, strain SD4 showed sustained growth at low concentrations of methane (100 and 500 ppmv). M. iwaonis SD4 could utilize diverse nitrogen sources, including nitrate, urea, ammonium as well as dinitrogen. Strain SD4 possessed genes encoding both the particulate methane monooxygenase and the soluble methane monooxygenase. Simple and rapid genetic manipulation methods were established for this strain, enabling vector transformation and unmarked genetic manipulation. Fast growth rate and efficient genetic tools make M. iwaonis SD4 an ideal model to study facultative methanotrophs, and the ability to grow on low concentration of methane implies its potential in methane removal. [ABSTRACT FROM AUTHOR]

Purpose: Arbuscular mycorrhizal fungi (AMF) perform an ancestral and essential association with plant roots, where plants provide carbohydrates and lipids, and the fungi respond by translocating water and nutrients to the roots through the hyphae. There is a need to investigate the microbial community associated with the rhizosphere of mycorrhizal plants in response to the multiple benefits (e.g., improved nutrition and stress resistance) provided by the association. In this work, we analyzed the bacterial communities associated with the rhizosphere of plants and their response to mycorrhizae in low P conditions. Methods: For this purpose, inoculated and non-inoculated B73 corn plants were grown with a consortium of mycorrhizal fungi under low phosphorus conditions. Mycorrhiza response in B73 and the interaction with rhizosphere microbiome were characterized by sequencing the bacterial 16S rRNA gene. Results: Inoculated plants showed increased greater growth in leaf and root parameters in low P conditions. Bacterial microbiome showed changes in beta diversity and some OUTs significantly regulated by AMF presence. Conclusion: These data confirm the importance of mycorrhizae in phosphorus stress and rhizosphere community changes as a possible mechanism to improve plant growth. [ABSTRACT FROM AUTHOR]

This study investigated the growth of Euphorbia tithymaloides L. in soil contaminated with Cr (VI), focusing on plant development, Cr (VI) accumulation in the plant, and associated rhizosphere bacterial communities. Plants were cultivated in pots for a period of 123 days with varying Cr (VI) levels (0, 10, 20, 30, and 40 mg-kg−1) in the soil. As Cr (VI) concentration increased, plant growth indicators such as fresh weight, dry weight, root length, and shoot length were observed to be decreasing. The Cr (VI) concentration peaked in plant tissues under the 40 mg-kg−1 treatment, with concentrations of 397.5 mg-kg−1, 98.12 mg-kg−1, and 62.32 mg-kg−1 in roots, stems, and leaves respectively. Whereas, the total Cr (VI) accumulation was maximum in the 30 mg-kg−1 treatment due to higher plant biomass. Further, the phytoremediation efficiency of the plant was evaluated through the bio-concentration factor (BCF) and translocation factor (TF). The BCF indicated soil-to-plant heavy metal uptake capacity exceeding 1, while the TF showed root-to-shoot translocation below 1 for all treatments, implying effective phytostabilisation potential. Metagenomic analysis of rhizospheric soil highlighted dominant bacterial phyla of Firmicutes, Proteobacteria, Bacteroidetes, Actinobacteria, and Acidobacteria. Many observed bacterial taxa are metal-tolerant and commonly found in heavy metal-contaminated soil, suggesting a potential contribution to mitigating metal toxicity and enhancing plant growth. However, a comprehensive investigation into microbial communities' roles during phytoremediation requires further in-depth research. [ABSTRACT FROM AUTHOR]

Deschampsia antarctica Desv. and Poa annua L. are two Poaceae plants with enough endurance to successfully establish populations in the Antarctic region. Their adaptation to the Antarctic environment is closely linked to root-associated microbial communities. In this study, we obtained 16S rRNA sequencing data of the root-associated microbial communities of these two Poaceae plants from NCBI. Meta-analysis was used to investigate the similarities and differences between the root endosphere and rhizosphere-dwelling microbial communities in these two Poaceae plants. Here we report that two Poaceae-Poaceae plants' rhizospheric communities were found to be more species diversity than endospheric communities. The species diversity of P. annua was higher than that of D. antarctica in both endosphere and rhizosphere communities. Seven bacterial families form a core microbiome of two Antarctic Poaceae plants' root endosphere, in which Microbacteriaceae appears to be obligatory root endophytes of the two Antarctic Poaceae plants. The core microbiome of the two Poaceae plants' rhizosphere has six bacterial families. Chitinophagaceae, Burkholderiaceae, and Flavobacteriaceae are most likely to play a crucial role in Poaceae plants' adaptation to cold Antarctic conditions. Sphingobacteriaceae, Caulobacteraceae, Gemmatimonadaceae, and Flavobacteriaceae have a great influence on two Antarctic Poaceae plants. [ABSTRACT FROM AUTHOR]

Phytoremediation is a technique for reducing or stabilizing hazardous chemicals in polluted soil or ground water. There is a loss of agricultural products and a degradation in food quality as a result of abiotic stresses, such as those generated by heavy metals and pesticides that have an effect on plants. These toxic compounds are extensively employed in agriculture, and they have a significant influence on both human health and agricultural output. The accumulation of these toxic, persistent, and poorly biodegradable compounds causes soil and ecological disparities. PGRs, or plant growth regulators, are an appealing possibility for increasing the efficacy of phytoremediation. Plant growth-promoting rhizobacteria (PGPR), a ubiquitous root microbiome, is widely used as a biocontrol agent. They have the ability to improve plant growth by colonizing plant roots, which can benefit the plant. Several PGPRs, including P. aeruginosa, B.gladioli, and P.pseudoalcali, have been shown to be resistant to biotic and abiotic stressors. Because of their ability to digest xenobiotic chemicals, plant growth-promoting rhizobacteria (PGPR) are a promising candidate for use in the phytoremediation process. Microorganisms inhabiting the rhizosphere participate in plant resistance mechanisms by secreting and generating a variety of important compounds such as siderophores, phytohormones, and metal-binding proteins. Rhizobacteria play an important role in phytoremediation of pesticide- and heavy metal-polluted soil by decomposing toxicants and promoting plant development via mechanisms such as chelation, acidification, and phosphate solubilization. Plant growth regulators (PGRs) increase plant biomass while reducing the negative impacts of contaminants and boosting growth in harsh settings. The use of certain PGRs as exogenous treatments have also been investigated as a potential way to improving crop stress tolerance; however the efficiency varies depending on the specific stress and plant type. Several plant growth regulators, such as brassinosteroids, melatonin, strigolactones, and others, have been proven to be useful in overcoming abiotic stress. The current review focuses on the utilization of PGRs and PGPRs in phytoremediation of heavy metal and pesticide-polluted soils. [ABSTRACT FROM AUTHOR]

The toxicity of cadmium (Cd) not only affects the growth and development of plants but also has an impact on human health. In this study, high-throughput sequencing and LC-MS were conducted to analyze the effect of CdCl2 treatment on the microbial community and soil metabolomics of rhizosphere soil in Rhododendron decorum subsp. diaprepes. The results showed that CdCl2 treatment reduced the quality of the rhizosphere soil by significantly decreasing the soil organic carbon (SOC) content, urease, and invertase activities, increasing the percentage of the exchangeable Cd fraction. CdCl2 treatment did not significantly change the Chao1 and Shannon indices of bacterial and fungal communities in the rhizosphere soil. R. decorum was more likely to recruit Cd-resistant bacteria (e.g., Proteobacteria, Chloroflexi) and increase the abundance of Cd-resistant fungi (e.g., Basidiomycota, Rozellomycota). Moreover, CdCl2 treatment decreased the content of secondary metabolites associated with plants' resistance to Cd. Rhizosphere soil urease, invertase activities, alkaline phosphatase (ALP), SOC, total potassium (TK), Cd, and nitrate nitrogen (NN) were the main drivers of the composition of rhizosphere bacterial and fungal communities. CdCl2 treatment weakened the relationships among bacterial/fungi, differential metabolites, and physicochemical properties in rhizosphere soil. [ABSTRACT FROM AUTHOR]

Wheat production is intrinsically linked to global food security. However, wheat cultivation is constrained by the progressive degradation of soil conditions resulting from the continuous application of fertilizers. This study aimed to examine the effects of deep tillage on rhizosphere soil microbial communities and their potential role in improving soil quality, given that the specific mechanisms driving these observed benefits remain unclear. Soil fertility in this research was evaluated through the analysis of various soil parameters, including total nitrogen, total phosphorus, total potassium, available phosphorus, and available potassium, among others. The high-throughput sequencing technique was utilized to examine the rhizosphere microbial community associated with deep tillage wheat. The findings indicated that deep tillage cultivation of wheat led to reduced fertility levels in the 0–20 cm soil layer in comparison with non-deep tillage cultivation. A sequencing analysis indicated that Acidobacteria and Proteobacteria are the dominant bacterial phyla, with Proteobacteria being significantly more abundant in the deep tillage group. The dominant fungal phyla identified were Ascomycota, Mortierellomycota, and Basidiomycota. Among bacterial genera, Arthrobacter, Bacillus, and Nocardioides were predominant, with Arthrobacter showing a significantly higher presence in the deep tillage group. The predominant fungal genera included Mortierella, Alternaria, Schizothecium, and Cladosporium. Deep tillage cultivation has the potential to enhance soil quality and boost crop productivity through the modulation of soil microbial community structure. [ABSTRACT FROM AUTHOR]