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Rapid urbanization has exerted immense pressure on urban environments, severely constraining the growth of ancient trees. The growth of ancient trees is closely linked to the microbial communities in their rhizospheres, and studying their community characteristics may provide new insights into promoting the growth and rejuvenation of ancient trees. In this study, the rhizosphere soil and root systems of ancient Ginkgo biloba trees (approximately 200 years old) and adult G. biloba trees (approximately 50 years old) in Shanghai were selected as research subjects. Phospholipid fatty acid (PLFA) analysis and high-throughput sequencing were employed to investigate the diversity of microbial communities in the G. biloba rhizosphere. The results indicated that the 19 PLFA species selected to characterize the soil microbial community structure and biomass were present in the rhizosphere soil of both ancient and adult G. biloba trees. However, the total microbial biomass and the microbial biomass in the rhizosphere soil of ancient G. biloba were lower than the microbial biomass in the rhizosphere soil of adult G. biloba. The biomasses of Gram-negative bacteria (G−), arbuscular mycorrhizal fungi (AMF), and protozoans (P) were significantly different. Total phosphorus, organic matter, and pH may be the key factors influencing the soil microbial community in the rhizosphere zone of ancient G. biloba. An in-depth study of AMF showed that the roots and rhizosphere soil of G. biloba contained abundant AMF resources, which were assigned to 224 virtual taxa using the MaarjAM reference database, belonging to four orders, ten families, and nineteen genera. The first and second most dominant genera were Glomus and Paraglomus, respectively. Archaeospora and Ambispora were more dominant in the rhizosphere than the roots. Furthermore, the abundance of live AMF was significantly higher in ancient G. biloba than in adult G. biloba. Therefore, future research should focus on the improvement of soil environmental characteristics and the identification and cultivation of indigenous dominant AMF in the rhizosphere of ancient G. biloba, aiming for their effective application in the rejuvenation of ancient trees. [ABSTRACT FROM AUTHOR]

Soil salinization during wheat cultivation considerably diminishes soil fertility and impedes wheat growth, primarily due to rhizosphere microbial community changes. Our study investigates the application of Bacillus subtilis YJ-15, a strain isolated from the rhizosphere of wheat cultivated in salinized soil, as a soil remediation agent. This strain has demonstrated significant salt tolerance, disease suppression capabilities, and growth-promoting attributes in previous studies. The wheat rhizosphere was examined to assess the impact of Bacillus subtilis YJ-15 on microbial community composition and soil fertility. Fertility of soil in saline soil was significantly increased by inoculating wheat with YJ-15. The microbial community structure within the wheat rhizosphere inoculated with Bacillus subtilis YJ-15 was analyzed through sequencing on the Illumina MiSeq platform. Phyla Proteobacteria and Acidobacteria were identified as the dominant bacteria. Basidiomycota, Mortierellomycota, and Ascomycota dominated the fungal phyla. Among the bacterial genera, Pseudomonas, Arthrobacter, and Bacillus were predominant. The predominant fungal genera included Alternaria, Cephalotrichum, Mortierella, and Chaetomium. A significant increase in Gaiella and Haliangium levels was observed in the YJ group compared to the control group. Additionally, the fungal genera Epicoccum, Sporidiobolus, and Lecythophora have significantly increased in YJ abundance. One of the potential benefits of Bacillus subtilis YJ-15 in the cultivation of wheat on salinized land is its ability to enhance the rhizosphere microbial community structure and improve soil fertility. [ABSTRACT FROM AUTHOR]

The objective of this study was to isolate and characterize actinobacteria from the rhizosphere of medicinal and aromatic plants, specifically lavender (Lavandula angustifolia Mill.), lemon balm (Melissa officinalis L.), and oregano (Origanum vulgare L.). Rhizospheric soil samples revealed a high abundance of culturable actinobacteria (6.97–7.23 log10 CFU/g). Six isolates were selected for their promising enzymatic activities (lignin peroxidase, carboxymethyl cellulase) and antimicrobial properties. Isolates M345 and M162 exhibited the highest cellulase activity indices (3.19 ± 0.71 and 2.54 ± 0.22, respectively), with five isolates producing lignin peroxidase. These actinobacteria also demonstrated plant growth-promoting traits such as phosphate solubilization and nitrogen fixation, along with strong antimicrobial activity against Gram-negative bacteria and phytopathogenic fungi. Additionally, they significantly enhanced maize seed germination, increasing the vigor index from 4283.33 ± 1264.37 to 6248.28 ± 1661.94 compared to that of the control. These results indicate that the isolated actinobacteria strains hold potential as microbial inoculants for sustainable agriculture, contributing to soil health, plant growth, and pathogen management. [ABSTRACT FROM AUTHOR]

To address the issue of phosphorus limitation in agricultural and forestry production and to identify green and economical alternatives to chemical phosphorus fertilizers, this paper reviews the utilization of phosphorus in plant–soil systems and explores the considerable potential for exploiting endogenous phosphorus resources. The application of phosphate-solubilizing microorganisms (PSMs) is emphasized for their role in phosphorus activation and plant growth promotion. A focus is placed on microbial interactions as an entry point to regulate the functional rhizosphere microbiome, introducing the concept of synthetic communities. This approach aims to deepen the understanding of PSM interactions across plant root, soil, and microbial interfaces, providing a theoretical foundation for the development and application of biological regulation technologies to enhance phosphorus utilization efficiency. [ABSTRACT FROM AUTHOR]

Plant-growth-promoting rhizobacteria (PGPR) play an important role in plant growth and rhizosphere soil. In order to evaluate the effects of PGPR strains on tea plant growth and the rhizosphere soil microenvironment, 38 PGPR strains belonging to the phyla Proteobacteria with different growth-promoting properties were isolated from the rhizosphere soil of tea plants. Among them, two PGPR strains with the best growth-promoting properties were then selected for the root irrigation. The PGPR treatment groups had a higher Chlorophyll (Chl) concentration in the eighth leaf of tea plants and significantly promoted the plant height and major soil elements. There were significant differences in microbial diversity and metabolite profiles in the rhizosphere between different experimental groups. PGPR improved the diversity of beneficial rhizosphere microorganisms and enhanced the root metabolites through the interaction between PGPR and tea plants. The results of this research are helpful for understanding the relationship between PGPR strains, tea plant growing, and rhizosphere soil microenvironment improvement. Moreover, they could be used as guidance to develop environmentally friendly biofertilizers with the selected PGPR instead of chemical fertilizers for tea plants. [ABSTRACT FROM AUTHOR]

Biodegradable microplastics (Bio-MPs) are a hot topic in soil research due to their potential to replace conventional microplastics. Biofertilizers are viewed as an alternative to inorganic fertilizers in agriculture due to their potential to enhance crop yields and food safety. The use of both can have direct and indirect effects on rhizosphere microorganisms. However, the influence of the coexistence of "Bio-MPs and biofertilizers" on rhizosphere microbial characteristics remains unclear. We investigated the effects of coexisting biofertilizers and Bio-MPs on the structure, function, and especially the carbon metabolic properties of crop rhizosphere bacteria, using a pot experiment in which polyethylene microplastics (PE-MPs) were used as a reference. The results showed that the existence of both microplastics (MPs) changed the physicochemical properties of the rhizosphere soil. Exposure to MPs also remarkably changed the composition and diversity of rhizosphere bacteria. The network was more complex in the Bio-MPs group. Additionally, metagenomic analyses showed that PE-MPs mainly affected microbial vitamin metabolism. Bio-MPs primarily changed the pathways related to carbon metabolism, such as causing declined carbon fixation/degradation and inhibition of methanogenesis. After partial least squares path model (PLS-PM) analysis, we observed that both materials influenced the rhizosphere environment through the bacterial communities and functions. Despite the degradability of Bio-MPs, our findings confirmed that the coexistence of biofertilizers and Bio-MPs affected the fertility of the rhizosphere. Regardless of the type of plastic, its use in soil requires an objective and scientifically grounded approach. [ABSTRACT FROM AUTHOR]

The rhizosphere is the hotspot for microbial enzyme activities and contributes to carbon cycling. Precipitation is an important component of global climate change that can profoundly alter belowground microbial communities. However, the impact of precipitation on conifer rhizospheric microbial populations has not been investigated in detail. In the present study, using high-throughput amplicon sequencing, we investigated the impact of precipitation on the rhizospheric soil microbial communities in two Norway Spruce clonal seed orchards, Lipová Lhota (L-site) and Prenet (P-site). P-site has received nearly double the precipitation than L-site for the last three decades. P-site documented higher soil water content with a significantly higher abundance of Aluminium (Al), Iron (Fe), Phosphorous (P), and Sulphur (S) than L-site. Rhizospheric soil metabolite profiling revealed an increased abundance of acids, carbohydrates, fatty acids, and alcohols in P-site. There was variance in the relative abundance of distinct microbiomes between the sites. A higher abundance of Proteobacteria, Acidobacteriota, Ascomycota, and Mortiellomycota was observed in P-site receiving high precipitation, while Bacteroidota, Actinobacteria, Chloroflexi, Firmicutes, Gemmatimonadota, and Basidiomycota were prevalent in L-site. The higher clustering coefficient of the microbial network in P-site suggested that the microbial community structure is highly interconnected and tends to cluster closely. The current study unveils the impact of precipitation variations on the spruce rhizospheric microbial association and opens new avenues for understanding the impact of global change on conifer rizospheric microbial associations. [ABSTRACT FROM AUTHOR]

As one of the most important fertilizers in agriculture, the fate of urea-derived nitrogen (urea-N) in agricultural ecosystems has been well documented. However, little is known about the function of urea-derived carbon (urea-C) in soil ecosystems, especially which soil microorganisms benefit most from the supply of urea-C and whether the utilization of urea-C by the rhizosphere and bulk soil microorganisms is affected by irrigation regimes. To address this, a soil pot experiment was conducted using 13C-labeled urea to investigate changes in the composition of the rhizosphere and bulk soil microbial communities and differences in the incorporation of urea-derived C into the rhizosphere and bulk soil phospholipid fatty acids (PLFA) pool under flooded irrigation (FI) and water-saving irrigation (CI). Our results suggest that the size and structure of the rhizosphere and bulk soil microbial communities were strongly influenced by the irrigation regime. The CI treatment significantly increased the total amount of PLFA in both the rhizosphere and bulk soil compared to the FI treatment, but it only significantly affected the abundance of Gram-positive bacteria (G+) in the bulk soil. In contrast, shifts in the microbial community structure induced by irrigation regimes were more pronounced in the rhizosphere soil than in the bulk soil. Compared to the FI treatment, the CI treatment significantly increased the relative abundances of the G+ and Actinobacteria in the rhizosphere soil (p < 0.05). According to the PLFA-SIP, most of the labeled urea-derived C was incorporated into 16:1ω7c, 16:0 and 18:1ω7c under both treatments. Despite these general trends, the pattern of 13C incorporation into the PLFA pool differed between the treatments. The factor loadings of individual PLFAs suggested that 18:1ω7c, 16:1ω7c and 16:1ω5c were relatively enriched in urea-C in the bulk soil, while 17:1ω8c, i16:0 and 16:0 were relatively enriched in urea-C in the rhizosphere soil under different irrigation regimes. The loadings also confirmed that 10-me16:0, cy17:0 and cy19:0 were relatively enriched in urea-C under the CI treatment, whereas 14:0, a15:0 and 15:0 were relatively enriched in urea-C under the FI treatment. These results are helpful not only in revealing the interception mechanism of urea-C in soil but also in understanding the functions of key microbes in element cycles. [ABSTRACT FROM AUTHOR]

Variations in the cadmium (Cd) accumulation and root characteristics of different genotypes of rice during three developmental periods of dry cultivation were investigated in pot experiments in which two levels of Cd were added to the soil (0 and 10 mg kg−1). The results show that the Cd concentration in each organ of the different rice genotypes decreased in both the order of roots > shoots > grains and during the three developmental periods in the order of the maturity stage > booting stage > tillering stage. The lowest bioaccumulation factor (BCF) and translocation factor (TF) were found in Yunjing37 (YJ37) under Cd stress. At maturity, Cd stress inhibited the root length of Dianheyou34 (DHY34) the most and that of Dianheyou 918 (DHY918) the least, also affecting the root volume of DHY34 and Dianheyou615 (DHY615) the most and that of YJ37 and Yiyou 673 (YY673) the least; the inhibition rates were 41.80, 5.09, 40.95, and 10.51%, respectively. The exodermis showed the greatest thickening in YY673 and the lowest thickening in DHY615, while the endodermis showed the opposite result. The rates of change were 16.48, 2.45, 5.10, and 8.49%, respectively. The stele diameter of DHY615 decreased the most, and that of YY673 decreased the least, while the secondary xylem area showed the opposite result; the rates of change were −21.50, −14.29, −5.86, and −26.35%, respectively. Under Cd stress treatment at maturity, iron plaque was extracted using the dithionite–citrate–bicarbonate (DCB) method. The concentration of iron (DCB-Fe) was highest in YJ37, and the concentration of cadmium (DCB-Cd) was lowest in DHY34. YJ37 was screened as a low Cd-accumulating variety. The concentration of available Cd in the rhizosphere soil, iron plaque, root morphology, and anatomy affect Cd accumulation in rice with genotypic differences. Our screening of Cd-accumulating rice varieties provides a basis for the dry cultivation of rice in areas with high background values of Cd in order to avoid the health risks of Cd intake. [ABSTRACT FROM AUTHOR]

The Hyphomicrobiales (Rhizobiales) order contains soil bacteria with an irregular distribution of the Calvin–Benson–Bassham cycle (CBB). Key enzymes in the CBB cycle are ribulose 1,5-bisphosphate carboxylase/oxygenase (RuBisCO), whose large and small subunits are encoded in cbbL and cbbS, and phosphoribulokinase (PRK), encoded by cbbP. These genes are often found in cbb operons, regulated by the LysR-type regulator CbbR. In Bradyrhizobium, pertaining to this order and bearing photosynthetic and non-photosynthetic species, the number of cbbL and cbbS copies varies, for example: zero in B. manausense, one in B. diazoefficiens, two in B. japonicum, and three in Bradyrhizobium sp. BTAi. Few studies addressed the role of CBB in Bradyrhizobium spp. symbiosis with leguminous plants. To investigate the horizontal transfer of the cbb operon among Hyphomicrobiales, we compared phylogenetic trees for concatenated cbbL-cbbP-cbbR and housekeeping genes (atpD-gyrB-recA-rpoB-rpoD). The distribution was consistent, indicating no horizontal transfer of the cbb operon in Hyphomicrobiales. We constructed a ΔcbbLS mutant in B. diazoefficiens, which lost most of the coding sequence of cbbL and has a frameshift creating a stop codon at the N-terminus of cbbS. This mutant nodulated normally but had reduced competitiveness for nodulation and long-term adhesion to soybean (Glycine max (L.) Merr.) roots, indicating a CBB requirement for colonizing soybean rhizosphere. [ABSTRACT FROM AUTHOR]

This study investigated the response of a bacterial community's structure and function in the rhizosphere soil of C3 and C4 plants under bis(2,4,6-tribromophenoxy) ethane (BTBPE) exposure. The bacterial community composition was determined using 16S rRNA sequencing, while FAPROTAX and PICRUSt 2 were employed for functional predictions. Results showed significant differences between C3 and C4 plants in terms of bacterial community structure. C3 plants exhibited higher abundances of Proteobacteria, Bacteroidetes at the phylum level and Sphingomicrobium at the genus level, compared to C4 plants. Conversely, C4 plants had higher abundances of Actinobacteria and Patescibacteria at the phylum level and Nocardioides at the genus level. LEfSe and function prediction analyses revealed that the rhizosphere soil bacteria in C3 plants exhibited significantly higher enrichment in nitrogen fixation functions (p < 0.05), whereas C4 plants showed a significantly higher relative abundance of bacteria and functions related to organic pollutant degradation (p < 0.05). These findings suggest that the rhizosphere soil bacteria of C3 plants exhibit a stronger response to BTBPE exposure in nitrogen metabolism-related processes, while C4 plants possess superior biodegradation ability compared to C3 plants. [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]

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]

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]

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]

Background: Urea fertilizer and MCPA herbicide are widely used agrochemicals in pastures. Even though urea hydrolysis impacts soil pH, potentially affecting MCPA dissipation, little is known about the effects of their co-application into the rhizosphere. Hence, we aimed to analyze the dynamics of urea transformation and MCPA dissipation when both are co-applied to the soil. Methods: A greenhouse experiment was conducted with a planted control and treatments incorporating urea and/or MCPA. Subsequently, pH changes, urea transformation into N-NH4+ and N-NO3−, the enzymatic activity of urease and dehydrogenase, and MCPA dissipation were monitored for 30 d. Results: Urea application induced a significant (p < 0.05) pH change, production of N-NH4+ (from 50 and 250 mg kg−1) and N-NO3− (from 206 to 347 mg kg−1), and urease (from 12 to 35 µmol N-NH4+g−1 h−1) and dehydrogenase (from 0.5 to 2.5 mg TPF g−1 h−1) activities. Urea also decelerated MCPA dissipation in the latter half of the experiment, whereas MCPA reduced urease activity when urea and herbicide were co-applied. Conclusions: Urea was the primary factor modifying the properties of the rhizosphere by stimulating the activity of microbial enzymes, shaping the pH changes during its mineralization, and decelerating MCPA dissipation. MCPA did not reduce urea mineralization but slowed urease activity, constituting an insight that requires further study. [ABSTRACT FROM AUTHOR]

Glomus mongioiense, a new species of arbuscular mycorrhizal fungi (AMF) in the family Glomeraceae, was isolated from rhizosphere soil collected from a meadow in the Italian Alps. The novelty of the species and its relationship with other species of the same genus were obtained by morphological and phylogenetic (45S nrDNA + RPB1 gene) analyses. Two glomoid spore-producing AMF isolates from a saltmarsh of the Scottish Highlands and maritime sand dunes of the Baltic Sea in Poland, were also included in this study and later found to be conspecific with G. rugosae. Phylogenetic placement analysis using environmental sequences indicated that G. mongioiense sp. nov. seems to be a rare species. Furthermore, the molecular and phylogenetic analysis provided important insights into the presence of highly divergent ribosomal variants in several Glomus species, with potential negative implication in phylogeny and species recognition. [ABSTRACT FROM AUTHOR]

Drought presents a significant abiotic stress that threatens crop productivity worldwide. Rhizosphere bacteria play pivotal roles in modulating plant growth and resilience to environmental stresses. Despite this, the extent to which rhizosphere bacteria are instrumental in plant responses to drought, and whether distinct cassava (Manihot esculenta Crantz) varieties harbor specific rhizosphere bacterial assemblages, remains unclear. In this study, we measured the growth and physiological characteristics, as well as the physical and chemical properties of the rhizosphere soil of drought-tolerant (SC124) and drought-sensitive (SC8) cassava varieties under conditions of both well-watered and drought stress. Employing 16S rDNA high-throughput sequencing, we analyzed the composition and dynamics of the rhizosphere bacterial community. Under drought stress, biomass, plant height, stem diameter, quantum efficiency of photosystem II (Fv/Fm), and soluble sugar of cassava decreased for both SC8 and SC124. The two varieties' rhizosphere bacterial communities' overall taxonomic structure was highly similar, but there were slight differences in relative abundance. SC124 mainly relied on Gamma-proteobacteria and Acidobacteriae in response to drought stress, and the abundance of this class was positively correlated with soil acid phosphatase. SC8 mainly relied on Actinobacteria in response to drought stress, and the abundance of this class was positively correlated with soil urease and soil saccharase. Overall, this study confirmed the key role of drought-induced rhizosphere bacteria in improving the adaptation of cassava to drought stress and clarified that this process is significantly related to variety. [ABSTRACT FROM AUTHOR]

DNA barcodes can provide accurate identification of plants. We used previously reported DNA primers targeting the internal transcribed spacer (ITS1) region of the nuclear ribosomal cistron, internal transcribed spacer (ITS2), and chloroplast trnL (UAA) intron to identify four trees at Bergen Community College. Two of the four trees were identified as Acer rubrum and Fagus sylvatica. However, Quercus was only identified at the genus level, and the fourth tree did not show similar identification between barcodes. Next-generation sequencing of 16S rRNA genes showed that the predominant bacterial communities in the rhizosphere mainly consisted of the Pseudomonadota, Actinomycetota, Bacteroidota, and Acidobacteriota. A. rubrum showed the most diverse bacterial community while F. sylvatica was less diverse. The genus Rhodoplanes showed the highest relative bacterial abundance in all trees. Fungal ITS sequence analysis demonstrated that the communities predominantly consisted of the Ascomycota and Basidiomycota. Quercus showed the highest fungi diversity while F. sylvatica showed the lowest. Russula showed the highest abundance of fungi genera. Average similarity values in the rhizosphere for fungi communities at the phylum level were higher than for bacteria. However, at the genus level, bacterial communities showed higher similarities than fungi. Similarity values decreased at lower taxonomical levels for both bacteria and fungi, indicating each tree has selected for specific bacterial and fungal communities. This study confirmed the distinctiveness of the microbial communities in the rhizosphere of each tree and their importance in sustaining and supporting viability and growth but also demonstrating the limitations of DNA barcoding with the primers used in this study to identify genus and species for some of the trees. The optimization of DNA barcoding will require additional DNA sequences to enhance the resolution and identification of trees at the study site. [ABSTRACT FROM AUTHOR]

Phosphorus constitutes a crucial macronutrient for crop growth, yet its availability often limits food production. Efficient phosphorus management is crucial for enhancing crop yields and ensuring food security. This study aimed to enhance the efficiency of a short-chain polyphosphate (PolyP) fertilizer by integrating it with plant growth-promoting bacteria (PGPB) to improve nutrient solubilization and wheat growth. Specifically, the study investigated the effects of various bacterial strains on wheat germination and growth when used in conjunction with PolyP. To achieve this, a greenhouse experiment was conducted in which the wheat rhizosphere was amended with a short-chain PolyP fertilizer. Based on the morphological aspect, eight bacteria, designated P1 to P8, were isolated and further characterized. Plant growth-promoting traits were observed in all bacterial strains, as they presented the ability to produce Indole Acetic Acid (IAA) in significant amounts ranging from 7.5 ± 0.3 µg/mL to 44.1 ± 2 µg/mL, expressed by B. tropicus P4 and P. soyae P1, respectively. They also produced ammonia, hydrogen cyanide (HCN), and siderophores. Their effect against the plant pathogen Fusarium culmorum was also assessed, with P. reinekei P2 demonstrating the highest biocontrol activity as it presented a total inhibitory effect. Additionally, some strains exhibited the ability to solubilize/hydrolyze phosphorus, potassium, and zinc. In vivo, the initial growth potential of wheat seeds indicated that those inoculated with the isolated strains exhibited elevated germination rates and enhanced root growth. Based on their plant growth-promoting traits and performance in the germination assay, three strains were selected for producing the best results, specifically phosphorus hydrolyzation/solubilization, zinc solubilization, IAA production, HCN, and siderophores production. Wheat seeds were inoculated by drenching in a bacterial suspension containing 1010 CFU/mL of log phase culture, and an in planta bioassay was conducted in a growth chamber using three selected strains (Pseudomonas soyae P1, Pseudomonas reinekei P2, and Bacillus tropicus P4), applied either individually or with PolyP on a P-deficient soil (28 mg/kg of P Olsen). Our findings demonstrated that the combination of Pseudomonas soyae P1 and PolyP achieved the highest shoot biomass, averaging 41.99 ± 0.87 g. Notably, applying P. soyae P1 or Bacillus tropicus P4 alone yielded similar results to the use of PolyP alone. At the heading growth stage, the combination of Bacillus tropicus P4 and PolyP significantly increased the Chlorophyll Content Index (CCI) to 37.02 µmol/m2, outperforming both PolyP alone (24.07 µmol/m2) and the control (23.06 µmol/m2). This study presents an innovative approach combining short-chain PolyP with bacterial biostimulants to enhance nutrient availability and plant growth. By identifying and characterizing effective bacterial strains, it offers a sustainable alternative to conventional fertilizers. [ABSTRACT FROM AUTHOR]

Seawater intrusion has a significant impact on the irrigation quality of agricultural water, thereby posing a threat to plant growth and development. We hypothesized that the rhizosphere of tea plants harbors beneficial microorganisms, which may improve the tolerance of tea plants to seawater stress. This study utilized 16s and ITS techniques to analyze microbial community shifts in the tea plant rhizosphere and non-rhizosphere under seawater stress conditions. The findings suggest that seawater stress leads to a reduction in microbial diversity, although the rhizosphere microbial diversity in stressed soils showed a relatively higher level. Moreover, the rhizosphere of the tea plant under seawater stress exhibited an enrichment of plant growth-promoting rhizobacteria alongside a higher presence of pathogenic fungi. Network analysis revealed that seawater stress resulted in the construction of a more complex and stable rhizosphere microbial network compared to normal conditions. Predictions of bacterial potential functions highlighted a greater diversity of functional groups, enhancing resource utilization efficiency. In general, the rhizosphere microorganisms of tea plants are jointly selected by seawater and the host. The microorganisms closely related to the rhizosphere of tea plants are retained and, at the same time, attract beneficial microorganisms that may alleviate stress. These findings provide new insights into plant responses to saline stress and have significant implications for leveraging vegetation to enhance the resilience of coastal saline soils and contribute to economic progress. [ABSTRACT FROM AUTHOR]

Clubroot is a soilborne disease of canola (Brassica napus) and other crucifers caused by the obligate parasite Plasmodiophora brassicae. In western Canada, clubroot is usually managed by planting-resistant cultivars, but the emergence of resistance-breaking pathotypes of P. brassicae represents a major threat to sustainable canola production. The rhizosphere and root contain beneficial microorganisms that can improve plant health. In this study, we evaluated the effect of two P. brassicae isolates (termed A and B) with different levels of virulence on the root and rhizosphere microbiomes of clubroot-resistant and clubroot-susceptible canola. Additionally, potential biocontrol microorganisms were identified based on taxa antagonistic to clubroot. Although both P. brassicae isolates were classified as pathotype 3A, isolate A caused a higher disease severity index in the resistant canola genotype compared with isolate B. Metabarcoding analysis indicated a shift in the bacterial and fungal communities in response to inoculation with either field isolate. Root endophytic bacterial and fungal communities responded to changes in inoculation, isolate type, sampling time, and canola genotype. In contrast, fungal communities associated with the rhizosphere exhibited significant differences between sampling times, while bacterial communities associated with the rhizosphere exhibited low variability. [ABSTRACT FROM AUTHOR]

This study aimed to highlight the positive effects of various recycled organic substrates on lettuce plants (Lactuca sativa L.) and to promote sustainable waste management practices, contributing to the concept of a circular economy. Over a two-month period, the growth potential and rhizosphere microflora of lettuce plants grown in soil amended with different recycled substrates were investigated. All data were compared, and the effects of the culture substrates were evaluated. All groups containing soil improvers offered a significant increase in the number of leaves per plant and, in two cases, an increase in dry biomass as well as an increase in the concentration of all leaf pigments. Both MDA and H2O2 concentrations were the lowest in two groups containing soil improvers (VG 5% and PLUS 10%). At the end of the culture period, isolation and culture of bacteria from the plant rhizosphere were performed. Different bacterial strains were isolated and tested for the production of antimicrobial agents against six microbial indicators (B. subtilis, E. coli, S. aureus, S. cerevisiae, C. albicans, and P. aeruginosa). The greater percentage of the isolated strains showed an ability to inhibit the growth of the B. subtilis index. Most of the strains with antimicrobial activity were isolated from the soil samples of the plain soil group and the soil amended with the commercial fertilizer. Three of the isolated strains originating from the Ginagro 5% group are multiproducers as they inhibit the growth of three microbial indicators or more. [ABSTRACT FROM AUTHOR]

There are obvious differences in quality between different varieties of the same plant, and it is not clear whether they can be effectively distinguished from each other from a bacterial point of view. In this study, 44 tea tree varieties (Camellia sinensis) were used to analyze the rhizosphere soil bacterial community using high-throughput sequencing technology, and five types of machine deep learning were used for modeling to obtain characteristic microorganisms that can effectively differentiate different varieties, and validation was performed. The relationship between characteristic microorganisms, soil nutrient transformation, and tea quality formation was further analyzed. It was found that 44 tea tree varieties were classified into two groups (group A and group B) and the characteristic bacteria that distinguished them came from 23 genera. Secondly, the content of rhizosphere soil available nutrients (available nitrogen, available phosphorus, and available potassium) and tea quality indexes (tea polyphenols, theanine, and caffeine) was significantly higher in group A than in group B. The classification result based on both was consistent with the above bacteria. This study provides a new insight and research methodology into the main reasons for the formation of quality differences among different varieties of the same plant. [ABSTRACT FROM AUTHOR]

Simple Summary: The sustainability of the tomato industry is increasingly debatable, necessitating innovative approaches to maximize productivity while minimizing environmental impact. The exploration of Synthetic Communities (SynComs) comprising nitrogen-fixing bacteria and mycorrhizal fungi represents a promising avenue toward achieving this balance. This work demonstrates that SynComs not only support tomato production under reduced fertilizer inputs, but also contribute to enhancing soil microbial biodiversity. This dual benefit underscores the potential of SynComs as a soil management strategy, offering a pathway toward sustainable agriculture and environmental stewardship. The agricultural sector is currently encountering significant challenges due to the effects of climate change, leading to negative consequences for crop productivity and global food security. In this context, traditional agricultural practices have been inadequate in addressing the fast-evolving challenges while maintaining environmental sustainability. A possible alternative to traditional agricultural management is represented by using beneficial micro-organisms that, once applied as bioinoculants, may enhance crop resilience and adaptability, thereby mitigating the adverse effects of environmental stressors and boosting productivity. Tomato is one of the most important crops worldwide, playing a central role in the human diet. The aim of this study was to evaluate the impact of a nitrogen-fixing bacterial-based biostimulant (Azospirillum sp., Azotobacter sp., and Rhizobium sp.) in combination or not with a commercial inoculum Micomix (Rhizoglomus irregulare, Funnelliformis mosseae, Funnelliformis caledonium, Bacillus licheniformis, and Bacillus mucilaginosus) (MYC) on the native rhizosphere communities and tomato production. Bacterial populations in the different samples were characterized using an environmental metabarcoding approach. The bioinocula effect on the native rhizosphere microbiota resulted in significant variation both in alpha and beta diversity and in a specific signature associated with the presence of biostimulants. [ABSTRACT FROM AUTHOR]

Sunflower broomrape (Orobanche cumana Wallr.) has severely restricted the development of the sunflower industry in China, and more efficient and convenient control methods are urgently needed. In this experiment, we investigated the effects of N, P and silica fertilizers on the parasitism rate of O. cumana, as well as on the yield of sunflower and native microbial communities in the field. Firstly, pot experiments were conducted to select the most effective fertilization method and to determine the physiological and biochemical indexes of sunflowers. Subsequently, field application studies were carried out to determine the physiological indexes, yield, O. cumana parasitism on sunflower, and the effect on the indigenous microbial community. The results demonstrate that compared with the CNP treatment (Control), the number of parasites under the N1P5 treatment significantly decreased by 66.15%. The exogenous application of silica can significantly reduce the number of O. cumana parasites. The treatments with N1P5 (N/P = 1:5) and available SiO2 content higher than 40 mg/kg (NS2, NS3, SF2 and SF3) significantly increased superoxide dismutase (SOD) activity and decreased malondialdehyde (MDA) content in sunflower leaves. In the field, fertilization significantly decreased the number of O. cumana parasites. The S treatment improved the native microbial community structure and enriched beneficial microorganisms, including Vicinamibacteria and Pyrinomonadaceae. Additionally, applying the S treatment significantly increased sunflower yield by 23.82% and crude protein content by 20.20%. In summary, the application of silicon fertilizer can effectively improve the host microbial community, reduce O. cumana parasitism and improve the yield and quality of sunflower. [ABSTRACT FROM AUTHOR]

Root-associated microorganisms, which can be recruited specially by plants to cope with environmental stress under extreme conditions, are one of the major mediators of nutrient exchange between plants and the environment. To obtain more crop-beneficial microbes, rhizosphere bacteria of Désirée potatoes cultivated in poor and alkaline soil have been studied. The screening of 83 strains with incomplete identical 16S rDNA sequences showed that 47 strains produced indole acetic acid (IAA), with contents ranging from 0.2 to 42 mg/L, and seven strains were phosphorus-solubilizing, among which six strains significantly increased the growth rate of potato plants. Thirty-seven strains produced siderophore and four strains were zinc-solubilizing, among which three strains significantly alleviated the chlorosis of potato plants. In all of the isolates, the species Variovorax soli (ST98) and Cellulomonas biazotea (ST118) were first found to possess an IAA-secreting ability; the species Leifsonia aquatica (ST172) and Leifsonia naganoensis (ST177) and the genus Sutcliffiella (ST11) were first discovered to be capable of phosphorus solubilization; the species Chryseobacterium daecheongense (ST32) was the first reported to be capable of zinc solubilization; and the species V. soli (ST98), C. biazotea (ST118) and L. naganoensis (ST177) were first found to be capable of plant growth promotion. The discovery of multiple functional bacteria enriched the resources of plant growth-promoting bacteria and provided a foundation for biofertilizer production to improve soil conditions and crop production. [ABSTRACT FROM AUTHOR]

The effects of companion planting on soil antibiotic resistance genes (ARGs) and associated microbial composition have remained largely unclear until now. In this study, we assessed the changes in the soil microbiome and ARGs frequencies for tomato growing soils that were companion planted with basil (TB) or cilantro (TC) using a metagenome approach. The abundance of the phytopathogen Ralstonia solanacearum was significantly lower in the TC or TB treatments compared to the tomato monoculture soils (TT). A significant enrichment of Pseudomonas and Aquabacterium and a depletion of Nocardioides and Streptomyces were observed in the TC treatment. Interestingly, both TC and TB companion planting reduced the absolute abundance and the number of subtypes of ARGs. The TC soil showed the lowest numbers of unique ARG subtypes, especially the ARGs resistant to vancomycin and rifamycin, as well as those associated with multidrug resistance. Furthermore, network analysis further revealed that Nocardioides and Streptomyces were potential hosts of ARGs, whereas Flavobacterium negatively correlated with mdtG, suggesting a suppressive effect in reducing ARGs. Together, our results suggest that the companion planting of tomatoes with basil or cilantro can reduce the risk of ARG accumulation, making it a feasible farming management tool to promote soil and plant health in sustainable agriculture. [ABSTRACT FROM AUTHOR]

The use of reclaimed wastewater to irrigate crops is a valuable option due to water scarcity. However, the presence of antibiotics residues that are not removed in the tertiary treatments reaches crop soils when irrigated and it poses a serious concern for human health. Crops rhizosphere is considered a hotspot of antibiotic resistant genes (ARG) being in addition a link to plant phyllosphere and human microbiome. Understanding the structure of the soil microbiota is crucial before applying any bioremediation or biostimulation strategy. The aim of this work was firstly to confirm the presence of antibiotics residues in soil and fruits in two greenhouses at the south of Spain irrigated with reclaimed water. Secondly, to characterize the rhizosphere microbiome of three crops (Capsicum annuum, Cucumis melo and Solanum melongena) cultured in those greenhouses. Finally, a predictive functional analysis was done using PICRUSt2 to figure out the rhizosphere resistome. The presence of residues of antibiotics was confirmed both soil and fruits. Antibiotics absorbed by plants correlated with those on soil. The most abundant resistance gene was the multidrug in all the three crops tested. Compatibility of basidiomycete fungi (i.e., Pleurotus) with soil bacteria could be indicative of their possible use for restoration of agricultural soils polluted with antibiotics. [ABSTRACT FROM AUTHOR]

A number of Phytophthora species have been identified as destructive plant pathogens and invasive species. They have the potential to affect a wide range of host plants and cause diseases in agricultural and forest ecosystems. Two Phytophthora species from rhizosphere soil samples collected from declining Alnus glutinosa in Bulgaria were isolated in the autumn of 2022. They were identified as Phytophthora polonica and Phytophthora hydropathica according to the DNA sequence analysis of the ITS region, as well as their morphological and physiological characteristics. The pathogenicity of both species to common and gray alder was evaluated by the inoculation of detached leaves and cuttings. Experimental data proved that P. polonica and P. hydropathica are able to cause leaf necrosis not only on A. glutinosa from which they were derived, but also on A. incana. No significant deference in the aggressiveness of the studied isolates from both Phytophthora species against the two tested plants was observed. Therefore, P. polonica and P. hydropathica were determined as potential threats for alder ecosystems in the country. This is the first report for the isolation of P. polonica in Bulgaria and represents the most southeastern point of the species distribution in Europe. [ABSTRACT FROM AUTHOR]

In order to further clarify the growth-promoting effect of the non-core Metarhizium sp. Marquandomyces marquandii on plants, M. marquandii SGSF043, which was obtained via pre-screening in the laboratory, was selected as a test strain and the seed soaking method was adopted. The effects of a fermentation broth obtained from this strain on the seed germination, seedling growth, and rhizosphere soil enzyme activity of maize were studied. The results were as follows: In seed germination tests, M. marquandii SGSF043 fermentation liquid had a certain inhibitory effect on corn seed germination, and the germination rate was only 15%. When the fermentation solution was diluted 10 times, the germination rate reached 97%. After the germination test, the growth of maize plumules was promoted in the groups treated with 10-times and 1000-times dilutions. In the field community experiment, based on the comprehensive evaluation of seedling biomass indicators, the solution diluted 100 times had the best growth-promoting effect. The aboveground fresh weight was increased by 127.13% compared with the control group. The results show that M. marquandii SGSF043 has the potential to promote the growth of maize and improve the soil environment, which provides a theoretical basis for the research on and the application of M. marquandii in farmland. [ABSTRACT FROM AUTHOR]

The rhizosphere of a plant is home to helpful microorganisms called plant growth-promoting rhizobacteria (PGPR), which play a crucial role in promoting plant growth and development. The significance of PGPR for long-term agricultural viability is outlined in this review. Plant growth processes such as nitrogen fixation, phosphate solubilization, and hormone secretion are discussed. Increased plant tolerance to biotic and abiotic stress, reduced use of chemical fertilizers and pesticides, and enhanced nutrient availability, soil fertility, and absorption are all mentioned as potential benefits of PGPR. PGPR has multiple ecological and practical functions in the soil's rhizosphere. One of PGPR's various roles in agroecosystems is to increase the synthesis of phytohormones and other metabolites, which have a direct impact on plant growth. Phytopathogens can be stopped in their tracks, a plant's natural defenses can be bolstered, and so on. PGPR also helps clean up the soil through a process called bioremediation. The PGPR's many functions include indole acetic acid (IAA) production, ammonia (NH3) production, hydrogen cyanide (HCN) production, catalase production, and more. In addition to aiding in nutrient uptake, PGPR controls the production of a hormone that increases root size and strength. Improving crop yield, decreasing environmental pollution, and guaranteeing food security are only some of the ecological and economic benefits of employing PGPR for sustainable agriculture. [ABSTRACT FROM AUTHOR]

Microbes and enzymes play essential roles in soil and plant rhizosphere ecosystem functioning. However, fungicides and plant root secretions may impact the diversity and abundance of microbiota structure and enzymatic activities in the plant rhizosphere. In this study, we analyzed soil samples from the rhizosphere of four cannabinoid-rich hemp (Cannabis sativa) cultivars (Otto II, BaOx, Cherry Citrus, and Wife) subjected to three different treatments (natural infection, fungal inoculation, and fungicide treatment). DNA was extracted from the soil samples, 16S rDNA was sequenced, and data were analyzed for diversity and abundance among different fungicide treatments and hemp cultivars. Fungicide treatment significantly impacted the diversity and abundance of the hemp rhizosphere microbiota structure, and it substantially increased the abundance of the phyla Archaea and Rokubacteria. However, the abundances of the phyla Pseudomonadota and Gemmatimonadetes were substantially decreased in treatments with fungicides compared to those without fungicides in the four hemp cultivars. In addition, the diversity and abundance of the rhizosphere microbiota structure were influenced by hemp cultivars. The influence of Cherry Citrus on the diversity and abundance of the hemp rhizosphere microbiota structure was less compared to the other three hemp cultivars (Otto II, BaOx, and Wife). Moreover, fungicide treatment affected enzymatic activities in the hemp rhizosphere. The application of fungicides significantly decreased enzyme abundance in the rhizosphere of all four hemp cultivars. Enzymes such as dehydrogenase, dioxygenase, hydrolase, transferase, oxidase, carboxylase, and peptidase significantly decreased in all the four hemp rhizosphere treated with fungicides compared to those not treated. These enzymes may be involved in the function of metabolizing organic matter and degrading xenobiotics. The ecological significance of these findings lies in the recognition that fungicides impact enzymes, microbiota structure, and the overall ecosystem within the hemp rhizosphere. [ABSTRACT FROM AUTHOR]

Microorganisms (MOs) are prominent in ecological functioning and balance. The rhizosphere is considered one of the most diverse ecosystems on Earth and serves as a breeding spot for many MOs. Rhizosphere microbial diversity changes according to plant species, genotype, and the nature of the soil. The current study reports the possible use of bacteria isolated from the rhizosphere of Azadirachta indica for synthesizing silver nanoparticles (AgNPs). The physicochemical characterization and antibacterial activity of these green synthesized AgNPs are also reported. The gene (16S rRNA) sequence of bacteria isolated from the rhizosphere showed a maximum similarity of 99.25% with Bacillus subtilis. After incubation, the colorless reaction mixture transformed to brown, which indicates the formation of AgNPs, and UV-vis spectral analysis also confirmed the biosynthesis of AgNPs. Compared to lower temperatures, the efficiency of AgNP synthesis was high at the higher temperature. The scanning electron microscope image demonstrated spherical-shaped AgNPs with sizes ranging from 18 to 21 nm. Energy-dispersive X-ray analysis established the elemental analysis of synthesized AgNPs. The synthesized AgNPs showed strong bactericidal properties against pathogenic bacteria Klebsiella pneumonia, Pseudomonas aeruginosa, Escherichia coli, and methicillin-resistant Staphylococcus aureus. [ABSTRACT FROM AUTHOR]

The rhizospheric microorganisms of agricultural crops play a crucial role in plant growth and nutrient cycling. In this study, we isolated two Streptomyces strains, Streptomyces sp. LM32 and Streptomyces sp. LM65, from the rhizosphere of Vitis vinifera L. We then conducted genomic analysis by assembling, annotating, and inferring phylogenomic information from the whole genome sequences. Streptomyces sp. strain LM32 had a genome size of 8.1 Mb and a GC content of 72.14%, while Streptomyces sp. strain LM65 had a genome size of 7.3 Mb and a GC content of 71%. Through ANI results, as well as phylogenomic, pan-, and core-genome analysis, we found that strain LM32 was closely related to the species S. coelicoflavus, while strain LM65 was closely related to the species S. achromogenes subsp. achromogenes. We annotated the functional categories of genes encoded in both strains, which revealed genes involved in nitrogen and phosphorus metabolism. This suggests that these strains have the potential to enhance nutrient availability in the soil, promoting agricultural sustainability. Additionally, we identified gene clusters associated with nitrate and nitrite ammonification, nitrosative stress, allantoin utilization, ammonia assimilation, denitrifying reductase gene clusters, high-affinity phosphate transporter and control of PHO regulon, polyphosphate, and phosphate metabolism. These findings highlight the ecological roles of these strains in sustainable agriculture, particularly in grapevine and other agricultural crop systems. [ABSTRACT FROM AUTHOR]

Ornamental horticulture and breeding, as well as urban landscape architecture, are facing increasing challenges driven by an intensely changing climate and urbanisation. The expansion of cities should be combined with an overall growth of green spaces, where ornamental plant species and cultivars will have to withstand a diverse range of environmental conditions, whereby they are often exposed to multiple stress factors. One of the most widely used ornamental shrub species Weigela florida 'Eva Rathke' was treated with the growth promoters Bistep with humic and fulvic acid, Kelpak® seaweed extract, and Yeald Plus with a high zinc content to test their applicability in a plant nursery. Bistep decreased the physiological parameters (the transpiration rate by 60%, the evapotranspiration rate by 56.5%, and the proline stress enzyme content level by 82.2%), indicating the stress level of the treated plants. The activity of β-glucosidase decreased with all growth-promoting treatments (11.5% for Kelpak and 9.5% for Yeald Plus), as did β-glucosaminidase (22.1% for Kelpak and 9.8% for Yeald Plus), but Bistep treatment reduced the activity of the enzymes less (9.9% for β-glucosidase and 3.3% for β-glucosaminidase). The measured alkaline phosphatase enzyme activity increased with treatment (by 10.7% for Kelpak, 11.7% for Yeald Plus, and 12.63% for Bistep). Based on the results, it was concluded that Bistep and Yeald Plus may be suitable for use in the studied variety, whereas Kelpak® may not be suggested in plant nurseries for growing W. florida 'Eva Rathke' plants. [ABSTRACT FROM AUTHOR]

Aquatic plants, just like terrestrial plants, are exposed to oxidative stress. However, their responses are still under-researched. In this study, we examined the physiological and antioxidative responses of an aquatic plant, duckweed (Lemna minor L.), to four indole-3-acetic acid (IAA)-degrading and -producing Pseudomonas bacteria (Pseudomonas oryzihabitans D1-104/3, P. putida A3-104/5, P. gessardii C31-106/3 and P. yamanorum C44-104/1) and/or a supraphysiological level of IAA (10 mg L−1). Growth characteristics, total photosynthetic pigment content, histochemical localization of reactive oxygen species and antioxidant enzyme activity (SOD, CAT and POX) were evaluated at two time points, after 3 and 7 days of co-cultivation. Superoxide anion and hydrogen peroxide were produced and accumulated mainly in the roots, daughter fronds and veins of duckweeds. Duckweeds' responses depended on the strain of Pseudomonas, time and exogenous IAA. Co-cultivation of duckweed with bacteria has positive or neutral effects. Exogenous application of IAA had a negative or neutral effect on enzyme activity and other parameters. Co-cultivation with P. gessardii C31-106/3 showed plant-growth-promoting effects on duckweed: increased biomass production, modulation of duckweeds' antioxidant enzymatic activity and reduction in hydrogen peroxide content. This study widens our knowledge of aquatic plants and their response to oxidative stress, supports the hypothesis that plant growth-promoting bacteria (PGPB) induce tolerable levels of oxidative stress in plants and introduces a new PGPB strain, P. gessardii C31-106/3. [ABSTRACT FROM AUTHOR]

Due to its adsorption with aluminum and iron hydroxides, phosphorus viability is low in acidic soils; thus, the aim of this study was to isolate and identify bacteria from the rhizosphere of four legumes growing in acidic soils of the Cumbaza Sub-basin, San Martín, Peru, as well as to characterize their ability to solubilize aluminum phosphate and iron phosphate. The isolation process was conducted on TSA medium and the isolates were classified based on their origin and morphocolonial characteristics, with the bacillary shape being the most frequent, followed by cocci. To assess the solubilization of aluminum and iron phosphates, the liquid medium GELP was employed. Sixteen strains were selected, among which three stood out for their effectiveness in solubilizing AlPO4 (Sfcv-098-02, 22.65 mg L−1; Sfc-093-04, 26.50 mg L−1; and Sfcv-041-01-2, 55.98 mg L−1) and one for its ability to solubilize FePO4 (Sfcr-043-02, 32.61 mg L−1). These four strains were molecularly characterized, being identified as Enterobacter sp., Pseudomonas sp., and Staphylococcus sp. Additionally, a decrease in pH was observed in the reactions, with values ranging from 5.23 to 3.29, which enhanced the phosphate of solubilization. This suggests that the selected bacteria could be used to improve phosphorus availability in agricultural soils. [ABSTRACT FROM AUTHOR]

Aims: Fokienia hodginsii is a threatened conifer tree species, known as the dominant nursery-grown species capable of colonizing the challenging woodland environments in southern China due to its strong root penetrating ability. The ecological phenotype of Fokienia hodginsii is not well documented during its breeding process, which limits the potential planting area and its ecological function. This study aims to understand how Fokienia hodginsii associates with microbes to conduct its key ecological function and provide a theoretical basis for further improving the forest nursery management of Fokienia hodginsii. Methods: This study explored the ecological traits of 11 main Fokienia hodginsii provenances in a homogeneous garden experiment by analyzing their nutrient utilization strategies and associated microbial features in the rhizosphere soil and roots. Results: The study found that the paramount difference in the rhizosphere soil among provenances is in Ca and Fe content. Some microbial communities, namely Crenarchaeota, Verrucomicrobiota, and Desulfobacterota, were positively correlated with the amounts of the soil nutrient elements, whereas Abditibacteriota and Dependentiae were negatively correlated. The abundance of N- and Fe-related bacteria in the Fu Jian Chang Ting (FJCT) provenance was significantly higher than that in other provenances, while the C-, P-, K-, and Mg-related fungal communities, respectively, had higher abundances in the FJCT, Fu Jian Long Yan (FJLY), Fu Jian Gu Tian (FJGT), and Fu Jian Xian You (FJXY) provenances than the others. The impacts of the Gui Zhou Li Ping (GZLP), Hu Nan Dao Xian (HNDX), Jiang Xi Shang Yao (JXSY), and Guang Dong Shi Xing (GDSX) provenances on the rhizosphere soil are similar, but the differences in nutrient utilization arise from the plant itself. Conversely, the root nutrient contents of the FJCT, Fu Jian You Xi (FJYX), Fu Jian An Xi (FJAX), FJLY, Fu Jian De Hua (FJDH), FJGT, and FJXY provenances are highly correlated with soil nutrient features. Conclusions: For the native provenances, their economic traits are better than the exotic provenances. The native provenances are more sensitive to local soil conditions, so they should benefit more from human interventions, rendering them more suitable for artificial cultivation. The growth of the exotic provenances is less affected by the soil environment, making them better suited for the ecological transformation of forest stands and soil improvement. [ABSTRACT FROM AUTHOR]

Cupressus gigantea is an endangered species mainly distributed on beach land, down-slope, and middle-slope positions along the Yarlung Zangbo River on the Tibet Plateau of China, with an altitude ranging from 3000 to 3400 m. We investigated the rhizosphere and fine root microbiomes of C. gigantea at these three slope positions through metagenomic analysis. Slope positions had a greater influence on microbiome composition in the rhizosphere than that in the fine roots. Down- and middle-slope positions presented higher microbial richness indeces and community similarity, while a more complex co-occurrence network was observed in the beach land samples. Rhizosphere bacterial community assembly was determined via deterministic processes in the beach land and via stochastic processes in the down- and middle-slope positions. Archaeal and fungal community assemblies were both dominated by stochastic processes in the rhizosphere and fine roots at the three slope positions. Nitrogen (N) functional genes were more sensitive to changes in slope positions than phosphorus (N) functional genes. Soil properties explained more than 60% and 34% of the variations in the N and P functional genes and more than 30% and 10% of the variations in the microbiomes in the rhizosphere and fine roots, respectively. Variation in the microbiome was significantly driven by total nirtogen, total potassium, pH, and soil moisture in rhizosphere, and by pH and soil moisture in fine roots. Our observations suggest that the effect of slope position on the microbiomes of C. gigantea was greater for the rhizosphere than the fine roots, with down- and middle-slope positions presenting higher community similarity. [ABSTRACT FROM AUTHOR]

The increase in industrialization has led to an exponential increase in heavy metal (HM) soil contamination, which poses a serious threat to public health and ecosystem stability. This review emphasizes the urgent need to develop innovative technologies for the environmental remediation of intensive anthropogenic pollution. Phytoremediation is a sustainable and cost-effective approach for the detoxification of contaminated soils using various plant species. This review discusses in detail the basic principles of phytoremediation and emphasizes its ecological advantages over other methods for cleaning contaminated areas and its technical viability. Much attention has been given to the selection of hyperaccumulator plants for phytoremediation that can grow on heavy metal-contaminated soils, and the biochemical mechanisms that allow these plants to isolate, detoxify, and accumulate heavy metals are discussed in detail. The novelty of our study lies in reviewing the mechanisms of plant–microorganism interactions that greatly enhance the efficiency of phytoremediation as well as in discussing genetic modifications that could revolutionize the cleanup of contaminated soils. Moreover, this manuscript discusses potential applications of phytoremediation beyond soil detoxification, including its role in bioenergy production and biodiversity restoration in degraded habitats. This review concludes by listing the serious problems that result from anthropogenic environmental pollution that future generations still need to overcome and suggests promising research directions in which the integration of nano- and biotechnology will play an important role in enhancing the effectiveness of phytoremediation. These contributions are critical for environmental scientists, policy makers, and practitioners seeking to utilize phytoremediation to maintain the ecological stability of the environment and its restoration. [ABSTRACT FROM AUTHOR]

Biostimulants and other plant growth promoters can provide an effective solution to the challenge of urbanisation and climate change. Viburnum opulus 'Roseum' is a globally popular deciduous shrub species that can be made more resistant to urban influences by using natural growth-promoting substances. In our study, we investigated the effects of growth promoters Kelpak®, Bistep and Yeald Plus on the species, both histologically and physiologically (proline stress hormone measurement). Our measurements were complemented using the analysis of rhizosphere alkaline phosphatase, β-glucosidase and β-glucosaminidase enzymes, to obtain a more complete picture of the combined effect of biostimulants and species. We found that the Bistep biostimulant had an outstanding effect on the leaf tissue culture results of the variety. The transpiration and evapotranspiration findings also confirmed the efficacy of biostimulants. In the case of POD activity and rhizosphere enzyme measurements, Bistep and Yeald Plus obtained statistically higher values than the control group. Kelpak produced better results than the control group in several measurements (alkaline phosphatase levels; evapotranspiration results), but in other cases it resulted in lower values than the control treatment. The use of Bistep and Yeald Plus can greatly assist growers in the cultivation of V. opulus 'Roseum' in an urban environment. [ABSTRACT FROM AUTHOR]

Pseudomonas chlororaphis ATCC 9446 is a non-pathogenic bacterium associated with the rhizosphere. It is commonly used as a biocontrol agent against agricultural pests. This organism can grow on a variety of carbon sources, has a robust secondary metabolism, and produces secondary metabolites with antimicrobial properties. This makes it an alternative host organism for synthetic biology applications. However, as a novel host there is a need for well-characterized molecular tools that allow fine control of gene expression and exploration of its metabolic potential. In this work we developed and characterized expression vectors for P. chlororaphis. We used two different promoters: the exogenously induced lac-IPTG promoter, and LuxR-C6-AHL, which we evaluated for its auto-inducible capacities, as well as using an external addition of C6-AHL. The expression response of these vectors to the inducer concentration was characterized by detecting a reporter fluorescent protein (YFP: yellow fluorescent protein). Furthermore, the violacein production operon was evaluated as a model heterologous pathway. We tested violacein production in shake flasks and a 3 L fermenter, showing that P. chlororaphis possesses a vigorous aromatic amino acid metabolism and was able to produce 1 g/L of violacein in a simple batch reactor experiment with minimal medium using only glucose as the carbon source. We compared the experimental results with the predictions of a modified genome scale model. The presented results show the potential of P. chlororaphis as a novel host organism for synthetic biology applications. [ABSTRACT FROM AUTHOR]

The synthesis of betalain using microorganisms is an innovative developmental technology, and the excavation of microorganisms closely related to betalain can provide certain theoretical and technical support to this technology. In this study, the characteristics of soil microbial community structures and their functions in the rhizospheres of white-fleshed dragon fruit (Hylocereus undatus) and red-fleshed dragon fruit (Hylocereus polyrhizus) were analyzed. The results show that the soil bacterial and fungal compositions in the rhizospheres were shaped differently between H. undatus and H. polyrhizus. Bacterial genera such as Kribbella and TM7a were the unique dominant soil bacterial genera in the rhizospheres of H. undatus, whereas Bradyrhizobium was the unique dominant soil bacterial genus in the rhizospheres of H. polyrhizus. Additionally, Myrothecium was the unique dominant soil fungal genus in the rhizospheres of H. polyrhizus, whereas Apiotrichum and Arachniotus were the unique dominant soil fungal genera in the rhizospheres of H. undatus. Moreover, TM7a, Novibacillus, Cupriavidus, Mesorhizobium, Trechispora, Madurella, Cercophora, and Polyschema were significantly enriched in the rhizospheres of H. undatus, whereas Penicillium, Blastobotrys, Phialemonium, Marasmius, and Pseudogymnoascus were significantly enriched in the rhizospheres of H. polyrhizus. Furthermore, the relative abundances of Ascomycota and Penicillium were significantly higher in the rhizospheres of H. polyrhizus than in those of H. undatus. [ABSTRACT FROM AUTHOR]

Plants significantly shape root-associated microbiota, making rhizosphere microbes useful environmental indicator organisms for safety assessment. Here, we report the pyrosequencing of the bacterial 16S ribosomal RNA in rhizosphere soil samples collected from transgenic cry1Ab/cry1Ac Bt rice Huahui No. 1 (GM crop) and its parental counterpart, Minghui63. We identified a total of 2579 quantifiable bacterial operational taxonomic units (OTUs). Many treatment-enriched microbial OTUs were identified, including 14 NonGM-enriched OTUs and 10 GM-enriched OTUs. OTUs belonging to the phyla Proteobacteria, Actinobacteria, Acidobacteria, Firmicutes, Nitrospirae, Chlorobi and GN04 were identified as statistically different in abundance between GM and the other two treatments. Compared with the different impacts of different rice varieties on microbiota, the impact of rice planting on microbiota is more obvious. Furthermore, Huahui No. 1 transgenic Bt rice had a greater impact on the rhizosphere bacterial communities than Minghui63. Early developmental stages of the transgenic Bt rice had a significant impact on many Bacillaceae communities. Soil chemical properties were not significantly altered by the presence of transgenic Bt rice. The peak concentration level of Bt protein products was detected during the seedling stage of transgenic Bt rice, which may be an intriguing factor for bacterial diversity variations. Based on these findings, we conclude that transgenic Bt rice has a significant impact on root-associated bacteria. This information may be leveraged in future environmental safety assessments of transgenic Bt rice varieties. [ABSTRACT FROM AUTHOR]

The American cranberry is a perennial North American fruit plant that is grown successfully on commercial plantations in Poland. The purpose of this study was to recognize filamentous fungi that colonize roots, leaves, and fruits without visible disease symptoms. Pure fungal cultures were isolated from disinfected plant fragments in agar media and identified by sequencing common taxonomic DNA markers such as the ITS region, the TEF-1α, or RPB2 genes. Of the 141 isolates studied, 59% were identified as closely related to soil saprotrophs. They were classified primarily as showing the greatest similarity to type strains of Trichoderma amoenum, Trichoderma dorothopsis, Paraphaeosphaeria sporulosa, and Penicillium murcianum. Additionally, isolates that are most similar to strains of Penicillium crustosum, Aspergillus flavus, and Aspergillus versicolor that produced mycotoxins were detected. The fungi identified as closest to Alternaria geophila, Alternaria senecionicola, Paraphoma radicina, Pestalotiopsis unicolor, Pestalotiopsis scoparia, and Neopestalotiopsis spp., whose hosts are plants other than American cranberry, represented 33.81% of the isolates tested. Only 7.2% of the isolates corresponded to the species of Physalospora vaccinia, Diaporthe vaccinii, and Diaporthe eres, known cranberry pathogens. The results of this study can be used to identify latent plant infection and potential disease risks. [ABSTRACT FROM AUTHOR]

Simple Summary: During the cultivation of medicinal plants, there may be some changes in the rhizosphere microenvironment. We used metagenomic sequencing analysis combined with metabolomics to investigate the composition, changes, and interactions of the microbial community structure and metabolites in rhizosphere soil during Fritillaria cirrhosa cultivation. The results showed that with the increase in cultivation years, the beneficial bacteria in the rhizosphere soil decreased while the harmful bacteria increased, and the relative content of some soil nutrients significantly decreased. The research results will provide guidance for the cultivation of Fritillaria cirrhosa. Fritillaria cirrhosa is an important cash crop, and its industrial development is being hampered by continuous cropping obstacles, but the composition and changes of rhizosphere soil microorganisms and metabolites in the cultivation process of Fritillaria cirrhosa have not been revealed. We used metagenomics sequencing to analyze the changes of the microbiome in rhizosphere soil during a three-year cultivation process, and combined it with LC-MS/MS to detect the changes of metabolites. Results indicate that during the cultivation of Fritillaria cirrhosa, the composition and structure of the rhizosphere soil microbial community changed significantly, especially regarding the relative abundance of some beneficial bacteria. The abundance of Bradyrhizobium decreased from 7.04% in the first year to about 5% in the second and third years; the relative abundance of Pseudomonas also decreased from 6.20% in the first year to 2.22% in the third year; and the relative abundance of Lysobacter decreased significantly from more than 4% in the first two years of cultivation to 1.01% in the third year of cultivation. However, the relative abundance of some harmful fungi has significantly increased, such as Botrytis, which increased significantly from less than 3% in the first two years to 7.93% in the third year, and Talaromyces fungi, which were almost non-existent in the first two years of cultivation, significantly increased to 3.43% in the third year of cultivation. The composition and structure of Fritillaria cirrhosa rhizosphere metabolites also changed significantly, the most important of which were carbohydrates represented by sucrose (48.00–9.36–10.07%) and some amino acid compounds related to continuous cropping obstacles. Co-occurrence analysis showed that there was a significant correlation between differential microorganisms and differential metabolites, but Procrustes analysis showed that the relationship between bacteria and metabolites was closer than that between fungi and metabolites. In general, in the process of Fritillaria cirrhosa cultivation, the beneficial bacteria in the rhizosphere decreased, the harmful bacteria increased, and the relative abundance of carbohydrate and amino acid compounds related to continuous cropping obstacles changed significantly. There is a significant correlation between microorganisms and metabolites, and the shaping of the Fritillaria cirrhosa rhizosphere's microecology by bacteria is more relevant. [ABSTRACT FROM AUTHOR]