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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]

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]

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]

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]

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]

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]

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]

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]

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]

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]

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]

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]

The article examines the fungal associates of the medicinal plant Acacia catechu in Hamirpur district in Himachal Pradesh, India. The study identifies the presence of species of the Arbuscular Mycorrhizal Fungi in the rhizosphere of Acacia catechu belonging to the genera Acaulospora, Gigaspora and Glomus, as well as endophytic fungal species belonging to the genera Aspergillus niger, Cladosporium cladosporioides and Fusarium solani.

The article investigates the fungal associates of medicinal plant Azadirachta indica A. Juss growing in district Una, Himachal Pradesh, India. The study identifies species of fungi from rhizosphere of Azadirachta indica, Arbascular Mycorrhizal Fungi belonging to the genera of Acaulospora, Gigaspora and Glomus, as well as the presence of endophytic fungi species belonging to the Fusarium, Gliocladium and Trichoderma genera.

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]

This study aimed to elucidate responses of the bacterial structure and diversity of the rhizosphere in flowering broomcorn millet after rehydration following drought stress. In this study, the broomcorn millet varieties 'Hequ red millet' (A1) and 'Yanshu No.10′ (A2), known for their different drought tolerance levels, were selected as experimental materials. The plants were subjected to rehydration after drought stress at the flowering stage, while normal watering (A1CK and A2CK) served as the control. Soil samples were collected at 10 days (A11, A21, A1CK1, and A2CK1) and 20 days (A12, A22, A1CK2, and A2CK2) after rehydration. High-throughput sequencing technology was employed to investigate the variations in bacterial community structure, diversity, and metabolic functions in the rhizosphere of the broomcorn millet at different time points following rehydration. The findings indicated that the operational taxonomic units (OTUs) of bacteria in the rhizosphere of broomcorn millet were notably influenced by the duration of treatment, with a significant decrease in OTUs observed after 20 days of rehydration. However, bacterial Alpha diversity was not significantly impacted by rehydration following drought stress. The bacterial community in the rhizosphere of broomcorn millet was mainly composed of Actinobacteria and Proteobacteria. After rewatering for 10 to 20 days after drought stress, the abundance of Sphingomonas and Aeromicrobium in the rhizosphere soil of the two varieties of broomcorn millet decreased gradually. Compared with Yanshu No.10, the abundance of Pseudarthrobacter in the rhizosphere of Hequ red millet gradually increased. A Beta diversity analysis revealed variations in the dissimilarities of the bacterial community which corresponded to different rehydration durations. The relative abundance of bacterial metabolic functions in the rhizosphere of broomcorn millet was lower after 20 days of rehydration, compared to measurements after 10 days of rehydration. This observation might be attributed to the exchange of materials between broomcorn millet and microorganisms during the initial rehydration stage to repair the effects of drought, as well as to the enrichment of numerous microorganisms to sustain the stability of the community structure. This study helps to comprehend the alterations to the bacterial structure and diversity in the rhizosphere of broomcorn millet following drought stress and rehydration. It sheds light on the growth status of broomcorn millet and its rhizosphere microorganisms under real environmental influences, thereby enhancing research on the drought tolerance mechanisms of broomcorn millet. [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]

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]

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]

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]

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]

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]

The close interconnection of plants with rhizosphere- and root-associated microorganisms is well recognized, and high expectations are raised for considering their symbioses in the breeding of future crop varieties. However, it is unclear how consistently plant-mediated selection, a potential target in crop breeding, influences microbiome members compared to selection imposed by the agricultural environment. Landraces may have traits shaping their microbiome, which were lost during the breeding of modern varieties, but knowledge about this is scarce. We investigated prokaryotic community composition along the radial root axis of two European maize (Zea mays L.) landraces. A sampling gradient included bulk soil, a distal and proximal rhizosphere fraction, and the root compartment. Our study was replicated at two field locations with differing edaphic and climatic conditions. Further, we tested for differences between two plant developmental stages and two precipitation treatments. Community data were generated by metabarcoding of the V4 SSU rRNA region. While communities were generally distinct between field sites, the effects of landrace variety, developmental stage, and precipitation treatment were comparatively weak and not statistically significant. Under all conditions, patterns in community composition corresponded strongly to the distance to the root. Changes in a- and b-diversity, as well as abundance shifts of many taxa along this gradient, were similar for both landraces and field locations. Most affected taxa belonged to a core microbiome present in all investigated samples. Remarkably, we observed consistent enrichment of Actinobacteriota (particularly Streptomyces, Lechevalieria) and Pseudomonadota (particularly Sphingobium) toward the root. Further, we report a depletion of ammoniaoxidizers along this axis at both field sites. We identified clear enrichment and depletion patterns in microbiome composition along the radial root axis of Z. mays. Many of these were consistent across two distinct field locations, plant developmental stages, precipitation treatments, and for both landraces. This suggests a considerable influence of plant-mediated effects on the microbiome. We propose that the affected taxa have key roles in the rhizosphere and root microbiome of Z. mays. Understanding the functions of these taxa appears highly relevant for the development of methods aiming to promote microbiome services for crops. [ABSTRACT FROM AUTHOR]

Plant-beneficial Pseudomonas bacteria hold the potential to be used as inoculants in agriculture to promote plant growth and health through various mechanisms. The discovery of new strains tailored to specific agricultural needs remains an open area of research. In this study, we report the isolation and characterization of four novel Pseudomonas species associated with the wheat rhizosphere. Comparative genomic analysis with all available Pseudomonas type strains revealed species-level differences, substantiated by both digital DNADNA hybridization and average nucleotide identity, underscoring their status as novel species. This was further validated by the phenotypic differences observed when compared to their closest relatives. Three of the novel species belong to the P. fluorescens species complex, with two representing a novel lineage in the Pseudomonas phylogeny. Functional genome annotation revealed the presence of specific features contributing to rhizosphere colonization, including flagella and components for biofilm formation. The novel species have the genetic potential to solubilize nutrients by acidifying the environment, releasing alkaline phosphatases and their metabolism of nitrogen species, indicating potential as biofertilizers. Additionally, the novel species possess traits that may facilitate direct promotion of plant growth through the modulation of the plant hormone balance, including the ACC deaminase enzyme and auxin metabolism. The presence of biosynthetic clusters for toxins such as hydrogen cyanide and nonribosomal peptides suggests their ability to compete with other microorganisms, including plant pathogens. Direct inoculation of wheat roots significantly enhanced plant growth, with two strains doubling shoot biomass. Three of the strains effectively antagonized fungal phytopathogens (Thielaviopsis basicola, Fusarium oxysporum, and Botrytis cinerea), demonstrating their potential as biocontrol agents. Based on the observed genetic and phenotypic differences from closely related species, we propose the following names for the four novel species: Pseudomonas grandcourensis sp. nov., type strain DGS24T (= DSM 117501T = CECT 31011T), Pseudomonas purpurea sp. nov., type strain DGS26T (= DSM 117502T = CECT 31012T), Pseudomonas helvetica sp. nov., type strain DGS28T (= DSM 117503T = CECT 31013T) and Pseudomonas aestiva sp. nov., type strain DGS32T (= DSM 117504T = CECT 31014T). [ABSTRACT FROM AUTHOR]

Allium hookeri is an indigenous perennial herb known for its therapeutic properties. It's grown in the eastern Himalayas and East Asia, where it is used as a flavoring agent in local cuisines. This research aims to enhance soil phosphorus mobilization and promote A. hookeri growth using a consortium of phosphate-solubilizing bacteria (PSB). The synergistic effect of a bacterial consortium containing multiple PSBs (Arthrobacter luteolus and several Klebsiella spp.) combined with tricalcium phosphate (TCP), was investigated to enhance the growth of A. hookeri plants, and its influence on modulating the rhizosphere microbiome was also assessed. The greenhouse experiment revealed that the bacterial consortium with tricalcium phosphate (BTCP) treatment enhanced the dry shoot weight by 70%. Proteobacteria dominated the rhizosphere's microbiome in all treatments. BTCP treatment enhanced the relative abundance of several beneficial genera such Bacillus, Mesorhizobium, Pseudomonas, Ensifer, Hyphomicrobium, Planctomyces, and Bradyrhizobium. The augmentation of bacterial consortium increased P in shoots (4.36 ± 0.63 mg/g) and in roots (2.34 ± 0.27 mg/g), which was more than 500% higher as compared to the uninoculated control. Canonical correspondence analysis (CCA) indicated significant correlations (p ≤ 0.05) between phosphorus content in the shoot, fresh weight, and dry weight, with higher relative abundances of Bacteroidetes, Cyanobacteria, and Fibrobacteres. Functional genes related to siderophore biosynthesis, ABC transporters, phosphatenate, and phosphinate metabolism exhibited positive modulation, indicating higher relative abundances associated with the BTCP treatment. The findings demonstrate the crucial contribution of the bacterial consortium in promoting plant development, improving soil nutrient levels, and influencing the rhizospheric microbiota, implying its significance in sustainable agriculture. [ABSTRACT FROM AUTHOR]

Mitigating the effects of climate stress on crops is important for global food security. The microbiome associated with plant roots, the rhizobiome, can harbor beneficial microbes that alleviate stress, but the factors influencing their recruitment are unclear. We conducted a greenhouse experiment using field soil with a legacy of growing switchgrass and common bean to investigate the impact of short-term drought severity on the recruitment of active bacterial rhizobiome members. We applied 16S rRNA and 16S rRNA gene sequencing for both crops and metabolite profiling for switchgrass. We included planted and unplanted conditions to distinguish environment- versus plant-mediated rhizobiome drivers. Differences in community structure were observed between crops and between drought and watered and planted and unplanted treatments within crops. Despite crop-specific communities, drought rhizobiome dynamics were similar across the two crops. The presence of a plant more strongly explained the rhizobiome variation in bean (17%) than in switchgrass (3%), with a small effect of plant mediation during drought observed only for the bean rhizobiome. The switchgrass rhizobiome was stable despite changes in rhizosphere metabolite profiles between planted and unplanted treatments. We conclude that rhizobiome responses to short-term drought are crop-specific, with possible decoupling of plant exudation from rhizobiome responses. In a study of short-term drought, the authors show an effect of plant mediation on the active rhizosphere microbiome of common bean, but not switchgrass. They conclude that microbiome responses are crop-specific and have possible decoupling of plant exudation and microbiome response. [ABSTRACT FROM AUTHOR]

Background: Guangxi is the leading sugarcane-producing area in China. Due to the Panama disease outbreak in banana gardens, sugarcane and banana rotation was recommended. A field experiment with the newly released sugarcane cultivar Zhongzhe 1 (ZZ1) was conducted to understand the role of the sugarcane–banana rotation system in shaping the rhizosphere microbiota. Fields in the region possess characteristics of red laterite soil. Results: Using Illumina HiSeq sequencing to analyze soil samples' 16S rRNA V3-V4 region, the preceding banana rotation field had relatively greater bacterial diversity than the monoculture sugarcane field. Proteobacteria, Chloroflexi, Actinobacteria, and Acidobacteria were the dominant phyla, with distinct taxa enriched in each environment. However, the preceding sugarcane monoculture field enriched functional groups related to nitrogen fixation and cellulolysis. Network analysis highlighted contrasting network structures between sugarcane and banana rhizospheres, suggesting differential stability and susceptibility to environmental influences. Furthermore, correlations between soil properties and bacterial alpha-diversity underscored the influence of preceding crops on rhizosphere microbial communities. Conclusion: This research enhances our understanding of crop rotation effects on soil microbial ecology and provides insights into optimizing agricultural practices for enhanced soil health and crop productivity. Future studies should explore the underlying mechanisms driving these interactions and evaluate the long-term impacts of crop rotation on soil microbial dynamics. [ABSTRACT FROM AUTHOR]

Water is an important constraint on alfalfa (Medicago sativa) production in arid and semiarid areas, and alternate irrigation in root areas has water-saving potential for alfalfa production. To investigate the impact of alternate partial root-zone irrigation (APRI) on the rhizosphere soil microorganisms of alfalfa, this study subjected alfalfa plants to different irrigation methods and irrigation levels. The growth status and rhizosphere soil microbial community diversity of alfalfa plants under alternate root-zone watering treatment were analyzed through laboratory experiments and high-throughput sequencing. The results showed that at soil moisture levels of 80% field moisture capacity (FMC) and 60% FMC, APRI had no significant impact on the biomass or nodule number of alfalfa. However, 40% FMC significantly reduced the individual plant dry weight, chlorophyll content, and nodule number of the alfalfa plants. APRI increased the relative abundance of Actinomycetes in the alfalfa rhizosphere soil. Moreover, at 60% FMC, the MBC and MBN of rhizosphere, relative abundance of Actinobacteria and unclassified K fungi and Chao 1 index of bacteria significantly increased under APRI treatment. While relative abundance of Ascomycetes and Proteobacteria in the alfalfa rhizosphere significantly reduced under 60% FMC + APRI treatment. In summary, under the same irrigation conditions, APRI did not significantly affect the growth of alfalfa in the short term. And 60%FMC + APRI treatment did significantly affect the groups, structure and diversity of the rhizosphere soil microbial communities. [ABSTRACT FROM AUTHOR]

Objective: Rhizosphere microorganisms play crucial roles in the growth and development of plants, disease resistance, and environmental adaptability. As the only wild pepper variety resource in China, domesticated Capsicum frutescens Linn. (Xiaomila) exhibits varying beneficial traits and affects rhizosphere microbial composition compared with its wild counterparts. In this study, we aimed to identify specific rhizosphere microbiome and metabolism patterns established during the domestication process. Methods: The rhizosphere microbial diversity and composition of domesticated and wild C. frutescens were detected and analyzed by metagenomics. Non-targeted metabolomics were used to explore the differences of metabolites in rhizosphere soil between wild and domesticated C. frutescens. Results: We found that the rhizosphere microbial diversity of domesticated variety was significantly different from that of the wild variety, with Massilia being its dominant bacteria. However, the abundance of certain beneficial microbes such as Gemmatimonas, Streptomyces, Rambibacter, and Lysobacter decreased significantly. The main metabolites identified in the wild variety included serylthreonine, deoxyloganic acid, vitamin C, among others. In contrast, those identified in the domesticated group were 4-hydroxy-L-glutamic acid and benzoic acid. Furthermore, the differentially enriched pathways were concentrated in tyrosine and tryptophan biosynthesis, histidine and purinederived alkaloids biosynthesis, benzoic acid family, two-component system, etc. Conclusion: This study revealed that C. frutescens established specific rhizosphere microbiota and metabolites during domestication, which has important significance for the efficient utilization of beneficial microorganisms in breeding and cultivation practices. [ABSTRACT FROM AUTHOR]

The bacterial microbiome plays crucial role in plants' resistance to diseases, nutrient uptake and productivity. We examined the microbiome characteristics of healthy and unhealthy strawberry farms, focusing on soil (bulk soil, rhizosphere soil) and plant (roots and shoots). The relative abundance of most abundant taxa were correlated with the chemical soil properties and shoot niche revealed the least amount of significant correlations between the two. While alpha and beta diversities did not show differences between health groups, we identified a number of core taxa (16–59) and marker bacterial taxa for each healthy (Unclassified Tepidisphaerales, Ohtaekwangia, Hydrocarboniphaga) and dysbiotic (Udaeobacter, Solibacter, Unclassified Chitinophagales, Unclassified Nitrosomonadaceae, Nitrospira, Nocardioides, Tardiphaga, Skermanella, Pseudomonas, Allorhizobium-Neorhizobium-Pararhizobium-Rhizobium, Curtobacterium) niche. We also revealed selective pressure of strawberry rhizosphere soil and roots plants in unhealthy plantations increased stochastic ecological processes of bacterial microbiome assembly in shoots. Our findings contribute to understanding sustainable agriculture and plant-microbiome interactions. [ABSTRACT FROM AUTHOR]

The interactions between plants and rhizosphere microbes mediated by plant root exudates are increasingly being investigated. The root-derived metabolites of medicinal plants are relatively diverse and have unique characteristics. However, whether medicinal plants influence their rhizosphere microbial community remains unknown. How medicinal plant species drive rhizosphere microbial community changes should be clarified. In this study involving high-throughput sequencing of rhizosphere microbes and an analysis of root exudates using a gas chromatograph coupled with a time-of-flight mass spectrometer, we revealed that the root exudate metabolites and microorganisms differed among the rhizosphere soils of five medicinal plants. Moreover, the results of a correlation analysis indicated that bacterial and fungal profiles in the rhizosphere soils of the five medicinal plants were extremely significantly or significantly affected by 10 root-associated metabolites. Furthermore, among the 10 root exudate metabolites, two (carvone and zymosterol) had opposite effects on rhizosphere bacteria and fungi. Our study findings suggest that plant-derived exudates modulate changes to rhizosphere microbial communities. [ABSTRACT FROM AUTHOR]

Four prenylated indole alkaloids (1−4) were targeted isolated from the mangrove rhizosphere soil-derived fungus Penicillium janthinellum HK1-6 by using molecular networking strategies. Among them, the planar structure and relative configuration of notoamide X (1) were elucidated by detailed analysis of the spectroscopic data especially the NOESY spectrum for the first time and its absolute configuration was determined by ECD spectrum. Furthermore, curated molecular networks of MS/MS data were generated with GNPS which allowed highlighting six prenylated indole alkaloids (5, 6, 8, 9, 11, 12) that had not previously been identified in this fungus and two (7, 10) that had never been observed in any fungus. The MS/MS fragmentation pathway of these prenylated indole alkaloids was summarized. [ABSTRACT FROM AUTHOR]

Introduction: The importance of plant rhizodeposition to sustain microbial growth and induce xenobiotic degradation in polluted environments is increasingly recognized. Methods: Here the "cry-for-help" hypothesis, consisting in root chemistry remodeling upon stress, was investigated in the presence of polychlorinated biphenyls (PCBs), highly recalcitrant and phytotoxic compounds, highlighting its role in reshaping the nutritional and signaling features of the root niche to accommodate PCB-degrading microorganisms. Results: Arabidopsis exposure to 70 µM PCB-18 triggered plant-detrimental effects, stress-related traits, and PCB-responsive gene expression, reproducing PCB phytotoxicity. The root exudates of plantlets exposed for 2 days to the pollutant were collected and characterized through untargeted metabolomics analysis by liquid chromatography-mass spectrometry. Principal component analysis disclosed a different root exudation fingerprint in PCB-18-exposed plants, potentially contributing to the "cry-for-help" event. To investigate this aspect, the five compounds identified in the exudate metabolomic analysis (i.e., scopoletin, N-hydroxyethyl-b-alanine, hypoxanthine, L-arginyl-L-valine, and Lseryl-L-phenylalanine) were assayed for their influence on the physiology and functionality of the PCB-degrading strains Pseudomonas alcaliphila JAB1, Paraburkholderia xenovorans LB400, and Acinetobacter calcoaceticus P320. Scopoletin, whose relative abundance decreased in PCB-18-stressed plant exudates, hampered the growth and proliferation of strains JAB1 and P320, presumably due to its antimicrobial activity, and reduced the beneficial effect of Acinetobacter P320, which showed a higher degree of growth promotion in the scopoletin-depleted mutant f6'h1 compared to Arabidopsis WT plants exposed to PCB. Nevertheless, scopoletin induced the expression of the bph catabolic operon in strains JAB1 and LB400. The primary metabolites hypoxanthine, Larginyl-L-valine, and L-seryl-L-phenylalanine, which increased in relative abundance upon PCB-18 stress, were preferentially used as nutrients and growth-stimulating factors by the three degrading strains and showed a variable ability to affect rhizocompetence traits like motility and biofilm formation. Discussion: These findings expand the knowledge on PCB-triggered "cry-forhelp" and its role in steering the PCB-degrading microbiome to boost the holobiont fitness in polluted environments. [ABSTRACT FROM AUTHOR]

Ginsengs, widely acknowledged for their health-promoting properties, are predominantly grown for their roots, necessitating an extended cultivation period of a minimum of 4 to 6 years for maturation. The prolonged growth duration in a specific location makes ginseng plants susceptible to soil-borne ailments, such as root rot, leading to significant detrimental effects. Focusing on the crucial role of the plant microbial community in maintaining ginseng health, the study reveals that repeated and continuous cultivation leads to the collapse of the initial disease-suppressive rhizosphere community, resulting in severe root rot. The dominance of Pseudomonadaceae in the rhizosphere subsequently reinstates disease suppression, aligning with suppressive soil generation phenomena. The research investigates the applicability of identified patterns to field conditions and demonstrates that rhizosphere samples from the field closely resemble conditions observed in pot-based NH4Cl treatment experiments. These findings emphasize the critical role of the rhizosphere microbial community in ginseng health maintenance during extended cultivation, offering insights into disease prevention strategies. The study also suggests the potential of pot-based experiments in simulating field conditions and informs future approaches for sustainable ginseng cultivation. [ABSTRACT FROM AUTHOR]

The rapid global emergence of antibiotic resistance genes (ARGs) is a substantial public health concern. Livestockmanure serves as a key reservoir for tetracycline resistance genes (TRGs), serving as a means of their transmission to soil and vegetables upon utilization as a fertilizer, consequently posing a risk to human health. The dynamics and transfer of TRGs among microorganisms in vegetables and fauna are being investigated. However, the impact of different vegetable species on acquisition of TRGs from various manure sources remains unclear. This study investigated the rhizospheres of three vegetables (carrots, tomatoes, and cucumbers) grown with chicken, sheep, and pigmanure to assess TRGs and bacterial community compositions via qPCR and high-throughput sequencing techniques. Our findings revealed that tomatoes exhibited the highest accumulation of TRGs, followed by cucumbers and carrots. Pig manure resulted in the highest TRG levels, compared to chicken and sheep manure, in that order. Bacterial community analyses revealed distinct effects of manure sources and the selective behavior of individual vegetable species in shaping bacterial communities, explaining 12.2% of TRG variation. Firmicutes had a positive correlation with most TRGs and the intl1 gene among the dominant phyla. Notably, both the types of vegetables andmanures significantly influenced the abundance of the intl1 gene and soil properties, exhibiting strong correlations with TRGs and elucidating 30% and 17.7% of TRG variance, respectively. Our study delineated vegetables accumulating TRGs from manure-amended soils, resulting in significant risk to human health. Moreover, we elucidated the pivotal roles of bacterial communities, soil characteristics, and the intl1 gene in TRG fate and dissemination. These insights emphasize the need for integrated strategies to reduce selection pressure and disrupt TRG transmission routes, ultimately curbing the transmission of tetracycline resistance genes to vegetables. [ABSTRACT FROM AUTHOR]

Plant–microbe interactions are essential in shaping plant performance and overall ecosystem functioning. However, the regulatory mechanisms underlying plant–microbe interactions mediated by mycorrhizal symbiosis in saline–alkaline soils are still not fully understood. Here, we aimed to clarify the synergistic regulatory mechanism through which arbuscular mycorrhizal fungi (AMF) symbiosis drives the rhizosphere microbiome to improve perennial herbage growth in saline–alkaline soils and evaluate phytoremediation efficiency. This study revealed that Funneliformis mosseae inoculation (i) strongly promoted the growth of all three herbage species (with values ranging from 21.62% to 233.33%), Na+ accumulation in plants (with values ranging from 24.63% to 188.89%), and decreased soil electrical conductivity (with values ranging from 7.68% to 12.87%), potentially suggesting improved phytoremediation efficiency with AMF symbiosis; (ii) increased nutritional content and decreased C:P and N:P ratios (with values ranging from 27.20% to 92.87%) and improved K+/Na+ and P/Na+ ratios (with values ranging from 2.60% to 302.96%); (iii) increased the abundance of some beneficial bacterial taxa and strengthened the significant strong relationships among most of these bacteria and plant biomass, ion homeostasis as well as stoichiometric ratio constants, and AMF inoculation treatments also consisted the higher proportion of differential genera significantly correlated with these plant factors as well as plant nutrient contents, potentially reflecting that AMF mediated the enrichment process of beneficial bacterial taxa and may strength functional interaction between plant and bacterial taxa, which may be importance for the enhancement of saline–alkaline tolerance of plants; and (iv) enhanced stability of the rhizosphere bacterial community and complexity of interaction networks, and the related indictors also established significant correlations with plant/soil factors, suggesting that the improvement of stability and functional complexity driven by AMF may also be beneficial for enhancing phytoremediation efficiency. These findings indicate that AMF inoculation plays its own beneficial role by simultaneously activating the potential of beneficial rhizosphere bacterial taxa and that their synergistic interaction is more beneficial for enhancing plant growth in salt‐affected soils and enhancing phytoremediation efficiency. This study helps to elucidate the underlying mechanisms through which AMF‐mediated rhizosphere bacterial community improve plant growth and tolerance to saline–alkaline stresses, and provides evidence that effective ecological restoration of saline–alkaline degraded grasslands can be achieved via the use of mycorrhizal symbiosis herbage. [ABSTRACT FROM AUTHOR]

Background: The rhizosphere microbiome displays structural and functional dynamism driven by plant, microbial, and environmental factors. While such plasticity is a well-evidenced determinant of host health, individual and community-level microbial activity within the rhizosphere remain poorly understood, due in part to the insufficient taxonomic resolution achieved through traditional marker gene amplicon sequencing. This limitation necessitates more advanced approaches (e.g., long-read sequencing) to derive ecological inferences with practical application. To this end, the present study coupled synthetic long-read technology with avidity sequencing to investigate eukaryotic and prokaryotic microbiome dynamics within the soybean (Glycine max) rhizosphere under field conditions. Results: Synthetic long-read sequencing permitted de novo reconstruction of the entire 18S-ITS1-ITS2 region of the eukaryotic rRNA operon as well as all nine hypervariable regions of the 16S rRNA gene. All full-length, mapped eukaryotic amplicon sequence variants displayed genus-level classification, and 44.77% achieved species-level classification. The resultant eukaryotic microbiome encompassed five kingdoms (19 genera) of protists in addition to fungi – a depth unattainable with conventional short-read methods. In the prokaryotic fraction, every full-length, mapped amplicon sequence variant was resolved at the species level, and 23.13% at the strain level. Thirteen species of Bradyrhizobium were thereby distinguished in the prokaryotic microbiome, with strain-level identification of the two Bradyrhizobium species most reported to nodulate soybean. Moreover, the applied methodology delineated structural and compositional dynamism in response to experimental parameters (i.e., growth stage, cultivar, and biostimulant application), unveiled a saprotroph-rich core microbiome, provided empirical evidence for host selection of mutualistic taxa, and identified key microbial co-occurrence network members likely associated with edaphic and agronomic properties. Conclusions: This study is the first to combine synthetic long-read technology and avidity sequencing to profile both eukaryotic and prokaryotic fractions of a plant-associated microbiome. Findings herein provide an unparalleled taxonomic resolution of the soybean rhizosphere microbiota and represent significant biological and technological advancements in crop microbiome research. [ABSTRACT FROM AUTHOR]