The structure and diversity of bacteria and fungi in the roots and rhizosphere soil of three different species of Geodorum.

Shepherd's crook (Geodorum) is a genus of protected orchids that are valuable both medicinally and ornamentally. Geodorum eulophioides (GE) is an endangered and narrowly distributed species, and Geodorum densiflorum (GD) and Geodorum attenuatum (GA) are widespread species. The growth of orchids depend on microorganisms. However, there are few studies on the microbial structure in Geodorum, and little is known about the roles of microorganisms in the endangered mechanism of G. eulophioides. This study analyzed the structure and composition of bacterial and fungal communities in the roots and rhizosphere soil of GE, GD, and GA. The results showed that Delftia, Bordetella and norank_f_Xanthobacteraceae were the dominant bacteria in the roots of Geodorum, while norank_f_Xanthobacteraceae, Gaiella and norank_f_norank_o_Gaiellales were the dominant bacteria in the rhizosphere soil of Geodorum. In the roots, the proportion of Mycobacterium in GD_roadside was higher than that in GD_understory, on the contrary, the proportion of Fusarium, Delftia and Bordetella in GD_roadside was lower than that in GD_understory. Compared with the GD_understory, the roots of GD_roadside had lower microbial diversity. In the endangered species GE, Russula was the primary fungus in the roots and rhizosphere soil, with fungal diversity lower than in the more widespread species. Among the widespread species, the dominant fungal genera in the roots and rhizosphere soil were Neocosmospora, Fusarium and Coprinopsis. This study enhances our understanding of microbial composition and diversity, providing fundamental information for future research on microbial contributions to plant growth and ecosystem function in Geodorum.

OsCIPK2 mediated rice root microorganisms and metabolites to improve plant nitrogen uptake.

Crop roots are colonized by large numbers of microorganisms, collectively known as the root-microbiome, which modulate plant growth, development and contribute to elemental nutrient uptake. In conditions of nitrogen limitation, the over-expressed Calcineurin B-like interacting protein kinase 2 (OsCIPK2) gene with root-specific promoter (RC) has been shown to enhance growth and nitrogen uptake in rice. Analysis of root-associated bacteria through high-throughput sequencing revealed that OsCIPK2 has a significant impact on the diversity of the root microbial community under low nitrogen stress. The quantification of nifH gene expression demonstrated a significant enhancement in nitrogen-fixing capabilities in the roots of RC transgenetic rice. Synthetic microbial communities (SynCom) consisting of six nitrogen-fixing bacterial strains were observed to be enriched in the roots of RC, leading to a substantial improvement in rice growth and nitrogen uptake in nitrogen-deficient soils. Forty and twenty-three metabolites exhibiting differential abundance were identified in the roots and rhizosphere soils of RC transgenic rice compared to wild-type (WT) rice. These findings suggest that OSCIPK2 plays a role in restructuring the microbial community in the roots through the regulation of metabolite synthesis and secretion. Further experiments involving the exogenous addition of citric acid revealed that an optimal concentration of this compound facilitated the growth of nitrogen-fixing bacteria and substantially augmented their population in the soil, highlighting the importance of citric acid in promoting nitrogen fixation under conditions of low nitrogen availability. These findings suggest that OsCIPK2 plays a role in enhancing nitrogen uptake by rice plants from the soil by influencing the assembly of root microbial communities, thereby offering valuable insights for enhancing nitrogen utilization in rice cultivation.

Community structure of soil microorganisms and endophytes of honeysuckle at different ecological niche specificities.

BACKGROUND: The plant microbiome is one of the key determinants of healthy plant growth. However, the complexity of microbial diversity in plant microenvironments in different regions, especially the relationship between subsurface and aboveground microorganisms, is not fully understood. The present study investigated the diversity of soil microorganisms in different regions and the diversity of microorganisms within different ecological niches, and compared soil microorganisms and endophytic microorganisms. METHODS: 16 S and ITS sequencing was used to sequence the soil and endophytes microbiome of honeysuckle. Alpha diversity analysis and principal component analysis (PCoA) were used to study the soil and endophyte microbial communities, and the function of endophyte bacteria and fungi was predicted based on the PICRUST2 process and FUNGuild. RESULTS: In total, there were 382 common bacterial genera and 139 common fungal genera in the soil of different producing areas of honeysuckle. There were 398 common bacterial genera and 157 common fungal genera in rhizosphere soil. More beneficial bacteria were enriched in rhizosphere soil. Endophytic bacteria were classified into 34 phyla and 770 genera. Endophytic fungi were classified into 11 phyla and 581 genera, among which there were significant differences in the dominant genera of roots, stems, leaves, and flowers, as well as in community diversity and richness. Endophytic fungal functions were mainly dominated by genes related to saprophytes, functional genes that could fight microorganisms were also found in KEGG secondary functional genes. CONCLUSION: More beneficial bacteria were enriched in rhizosphere soil of honeysuckle, and the microbial network of the rhizosphere is more complex than that of the soil. Among the tissues of honeysuckle, the flowers have the richest diversity of endophytes. The endogenous dominant core bacteria in each part of honeysuckle plant have a high degree of overlap with the dominant bacteria in soil. Functional prediction suggested that some dominant core bacteria have antibacterial effects, providing a reference for further exploring the strains with antibacterial function of honeysuckle. Understanding the interaction between honeysuckle and microorganisms lays a foundation for the study of growth promotion, quality improvement, and disease and pests control of honeysuckle from the perspective of microorganisms.

Description of Microbacterium dauci sp. nov., a plant growth hormone indoleacetic acid-producing and nitrogen-fixing bacterium isolated from carrot rhizosphere soil.

A plant growth hormone indoleacetic acid-producing strain LX3-4T was isolated from a carrot rhizosphere soil sample collected in Shandong Province, China. It is Gram-stain-positive, non-motile, and has irregular short rod-shaped cells. LX3-4T shared high 16S rRNA gene sequence identity with Microbacterium oleivorans DSM 16091T (99.4%), M. testaceum NBRC 12675T (98.6%), M. marinum DSM 24947T (98.5%), M. resistens NBRC 103078T (98.4%), and M. paraoxydans NBRC 103076T (98.3%). Phylogenetic analysis based on the concatenated gene sequences of 16S rRNA gene, housekeeping genes gryB and rpoB also showed the distinction between strain LX3-4T and other Microbacterium species. Furthermore, analysis of the average nucleotide identities (ANI), the average amino acid identity (AAI), and the digital DNA-DNA hybridization (dDDH) values between strain LX3-4T and its relatives revealed that strain LX3-4T represents a distinct species. The genomic DNA G + C content of the strain is 69.5%. It can grow at 25-37 °C (optimum 37 °C), pH 5.0-10.0 (optimum pH 6.0-8.0), and the range of NaCl concentration is 0-7% (w/v) (optimum 1-5%). The colonies on agar plates are smooth, translucent, and pale yellow. The main cellular fatty acids of strain LX3-4T are anteiso-C15:0, anteiso-C17:0, and iso-C16:0. The predominant respiratory quinones are MK-12 and MK-11. Diphosphatidylglycerol, phosphatidylglycerol, an unidentified glycolipid, and an unidentified phosphoglycolipid are major polar lipids. The cell-wall sugar of strain LX3-4T is glucose. The cell-wall peptidoglycan contains glycine, alanine, lysine, and glutamic acid. In addition, this strain carries nitrogen fixation genes and can grow in nitrogen-free medium. Based on the polyphasic data, strain LX3-4T represents a novel species of the genus Microbacterium, for which the name Microbacterium dauci sp. nov. is proposed with strain LX3-4T (= CCTCC AB 2023103T = LMG 33159T) designated as the type strain.

Deinococcus rhizophilus sp.nov., isolated from rhizosphere soil.

A spherical, pink, aerobic, Gram-stain-positive bacterial strain (MIMF12T) was isolated from rhizosphere soil collected in the Inner Mongolia Autonomous Region, PR China. Cellular growth of the strain was observed at pH 6.0-8.0 (optimum, pH 7.0), at 20-37 °C (optimum, 28 °C) and with 0-1 % (w/v) NaCl (optimum, 0 %). Phylogenetic analyses based on 16S rRNA gene sequences indicated that strain MIMF12T was most closely related to Deinococcus terrestris SDU3-2T with a similarity value of 96.0 %. The respiratory quinone was menaquinone 8, the major fatty acids were C15 : 1 ω6c and C17 : 1 ω8c, and the major polar lipids were composed of two aminophospholipids, one phospholipid and four unidentified lipids. The G+C content of the genomic DNA was 70.1 mol%. The average nucleotide identity and digital DNA-DNA hybridization values between strain MIMF12T and the closest related type strain SDU3-2T were 88.1 and 52.1 %, respectively. The discovery that MIMF12T differs not only from validly named species in the genus Deinococcus, but also from currently unnamed species in the GDTB, gives us new insights into the genus. Based on phenotypic, chemotaxonomic and phylogenetic characteristics, strain MIMF12T represents a novel species of the genus Deinococcus, for which the name Deinococcus rhizophilus sp. nov. is proposed. The type strain is MIMF12T (=CGMCC 1.61579T=KCTC 43572T).

Sinomonas terricola sp. nov., a plant-beneficial bacterium isolated from litchi rhizosphere soil in Guangdong, China.

A novel plant-beneficial bacterium strain, designated as JGH33T, which inhibited Peronophythora litchii sporangia germination, was isolated on Reasoner's 2A medium from a litchi rhizosphere soil sample collected in Gaozhou City, Guangdong Province, PR China. Cells of strain JGH33T were Gram-stain-positive, aerobic, non-motile, bent rods. The strain grew optimally at 30-37 °C and pH 6.0-8.0. Sequence similarity analysis based on 16S rRNA genes indicated that strain JGH33T exhibited highest sequence similarity to Sinomonas albida LC13T (99.2 %). The genomic DNA G+C content of the isolate was 69.1 mol%. The genome of JGH33T was 4.7 Mbp in size with the average nucleotide identity value of 83.45 % to the most related reference strains, which is lower than the species delineation threshold of 95 %. The digital DNA-DNA hybridization of the isolate resulted in a relatedness value of 24.9 % with its closest neighbour. The predominant respiratory quinone of JGH33T was MK-9(H2). The major fatty acids were C15 : 0 anteiso (43.4 %), C16 : 0 iso (19.1 %) and C17 : 0 anteiso (19.3 %), and the featured component was C18 : 3 ω6c (1.01 %). The polar lipid composition of strain JGH33T included diphosphatidylglycerol, phosphatidylglycerol, dimannosylglyceride, phosphatidylinositol and glycolipids. On the basis of polyphasic taxonomy analyses data, strain JGH33T represents a novel species of the genus Sinomonas, for which the name Sinomonas terricola sp. nov. is proposed, with JGH33T (=JCM 35868T=GDMCC 1.3730T) as the type strain.

Foliar Application of Nanoparticles Reduced Cadmium Content in Wheat (Triticum aestivum L.) Grains via Long-Distance "Leaf-Root-Microorganism" Regulation.

Foliar application of beneficial nanoparticles (NPs) exhibits potential in reducing cadmium (Cd) uptake in crops, necessitating a systematic understanding of their leaf-root-microorganism process for sustainable development of efficient nano-enabled agrochemicals. Herein, wheat grown in Cd-contaminated soil (5.23 mg/kg) was sprayed with different rates of four commonly used NPs, including nano selenium (SeNPs)/silica (SiO2NPs)/zinc oxide/manganese dioxide. SeNPs and SiO2NPs most effectively reduced the Cd concentration in wheat grains. Compared to the control, Cd concentration in grains was significantly decreased by 35.0 and 33.3% by applying 0.96 mg/plant SeNPs and 2.4 mg/plant SiO2NPs, and the grain yield was significantly increased by 33.9% with SeNPs application. Down-regulated gene expression of Cd transport proteins (TaNramp5 and TaLCT1) and up-regulated gene expression of vacuolar Cd fixation proteins (TaHMA3 and TaTM20) were observed with foliar SeNPs and SiO2NPs use. SeNPs increased the levels of leaf antioxidant metabolites. Additionally, foliar spray of SeNPs resulted in lower abundances of rhizosphere organic acids and reduced Cd bioavailability in rhizosphere soil, and soil microorganisms related to carbon and nitrogen (Solirubrobacter and Pedomicrobium) were promoted. Our findings underscore the potential of the foliar application of SeNPs and SiO2NPs as a plant and rhizosphere soil metabolism-regulating approach to reduce Cd accumulation in wheat grains.

Straw application improved soil biological properties and the growth of rice plant under low water irrigation.

The application of organic amendments is one way to manage low water irrigation in paddy soils. In this 60-day greenhouse pot experiment involving paddy soil undergoing drying-rewetting cycles, we examined the effects of two organic amendments: azo-compost with a low carbon to phosphorus ratio (C:P) of 40 and rice straw with a high C:P ratio of 202. Both were applied at rates of 1.5% of soil weight (w/w). The investigation focused on changes in certain soil biochemical characteristics related to C and P in the rice rhizosphere, as well as rice plant characteristics. The irrigation regimes applied in this study included constant soil moisture in a waterlogged state (130% water holding capacity (WHC)), mild drying-rewetting (from 130 to 100% WHC), and severe drying-rewetting (from 130 to 70% WHC). The results indicated that the application of amendments was effective in severe drying-rewetting irrigation regimes on soil characteristics. Drying-rewetting decreased soil respiration rate (by 60%), microbial biomass carbon (by 70%), C:P ratio (by 12%), soil organic P (by 16%), shoot P concentration (by 7%), and rice shoot biomass (by 30%). However, organic amendments increased soil respiration rate (by 8 times), soil microbial biomass C (51%), total C (TC) (53%), dissolved organic carbon (3 times), soil available P (AP) (100%), soil organic P (63%), microbial biomass P (4.5 times), and shoot P concentration (21%). The highest significant correlation was observed between dissolved organic carbon and total C (r= 0.89**). Organic amendments also increased P uptake by the rice plant in the order: azo-compost > rice straw > control treatments, respectively, and eliminated the undesirable effect of mild drying-rewetting irrigation regime on rice plant biomass. Overall, using suitable organic amendments proves promising for enhancing soil properties and rice growth under drying-rewetting conditions, highlighting the interdependence of P and C biochemical changes in the rhizosphere during the rice vegetative stage.

Zonation of bulk and rhizosphere soil bacterial communities and their covariation patterns along the elevation gradient in riparian zones of three Gorges reservoir, China.

Zonation is a typical pattern of soil distribution and species assembly across riparian habitats. Microorganisms are essential members of riparian ecosystems and whether soil microbial communities demonstrate similar zonation patterns and how bulk and rhizosphere soil microorganisms interact along the elevation (submergence stress) gradient remain largely unknown. In this study, bulk and rhizosphere (dominant plant) soil samples were collected and investigated across riparian zones where the submergence stress intensity increased as the elevation decreased. Results showed that the richness of bacterial communities in bulk and rhizosphere soil samples was significantly different and presented a zonation pattern along with the submergence stress gradient. Bulk soil at medium elevation that underwent moderate submergence stress had the most abundant bacterial communities, while the species richness of rhizobacteria at low elevation that experienced serious submergence stress was the highest. Additionally, principal coordinate analysis (PCoA) and significance tests showed that bulk and rhizosphere soil samples were distinguished according to the structure of bacterial communities, and so were bulk or rhizosphere soil samples from different elevations. Redundancy analysis (RDA) and Mantel test suggested that bacterial communities of bulk soil mainly relied on the contents of soil organic matter, total carbon (TC), total nitrogen (TN), sodium (Na), calcium (Ca) and magnesium (Mg). Contrastingly, the contents of Na and Mg were the main factors explaining the variation in rhizobacterial community composition. Correlation and microbial source tracking analyses showed thatthe relationship of bulk and rhizosphere soil bacteria became much stronger, and the rhizosphere soil may get more bacterial communities from bulk soil with the increase in submergence severity. Our results suggest that the abiotic and biotic components of the riparian ecosystem are closely covariant along the submergence stress gradient and imply that the bacterial community may be a key node linking soil physiochemical properties and vegetation communities.

Metagenomic approach reveals the role of bioagents in the environmental dissemination risk of rhizosphere soil antibiotic resistance genes pollution.

Antibiotic resistance genes (ARGs) have been identified as emerging contaminants, raising concerns around the world. As environmentally friendly bioagents (BA), plant growth-promoting rhizobacteria (PGPR) have been used in agricultural systems. The introduction of BA will lead to the turnover of the microbial communities structure. Nevertheless, it is still unclear how the colonization of the invaded microorganisms could affects the rhizosphere resistome. Consequently, 190 ARGs and 25 integrative and conjugative elements (ICEs) were annotated using the metagenomic approach in 18 samples from the Solanaceae crop rhizosphere soil under BA and conventional treatment (CK) groups. Our study found that, after 90 days of treatment, ARG abundance was lower in the CK group than in the BA group. The results showed that aminoglycoside antibiotic resistance (OprZ), phenicol antibiotic resistance (OprN), aminoglycoside antibiotic resistance (ceoA/B), aminocoumarin antibiotic resistance (mdtB) and phenicol antibiotic resistance (MexW) syntenic with ICEs. Moreover, in 11 sequences, OprN (phenicol antibiotic resistance) was observed to have synteny with ICEPaeLESB58-1, indicating that the ICEs could contribute to the spread of ARGs. Additionally, the binning result showed that the potential bacterial hosts of the ARGs were beneficial bacteria which could promote the nutrition cycle, such as Haliangium, Nitrospira, Sideroxydans, Burkholderia, etc, suggesting that bacterial hosts have a great influence on ARG profiles. According to the findings, considering the dissemination of ARGs, BA should be applied with caution, especially the use of beneficial bacteria in BA. In a nutshell, this study offers valuable insights into ARGs pollution control from the perspective of the development and application of BA, to make effective strategies for blocking pollution risk migration in the ecological environment.

Genetic control of rhizosphere microbiome of the cotton plants under field conditions.

Understanding the extent of heritability of a plant-associated microbiome (phytobiome) is critically important for exploitation of phytobiomes in agriculture. Two crosses were made between pairs of cotton cultivars (Z2 and J11, L1 and Z49) with differential resistance to Verticillium wilt. F2 plants were grown in a field, together with the four parents to study the heritability of cotton rhizosphere microbiome. Amplicon sequencing was used to profile bacterial and fungal communities in the rhizosphere. F2 offspring plants of both crosses had higher average alpha diversity indices than the two parents; parents differed significantly from F2 offspring in Bray-Curtis beta diversity indices as well. Two types of data were used to study the heritability of rhizosphere microbiome: principal components (PCs) and individual top microbial operational taxonomic units (OTUs). For the L1 × Z49 cross, the variance among the F2 progeny genotypes (namely, genetic variance, VT) was significantly greater than the random variability (VE) for 12 and 34 out of top 100 fungal and bacterial PCs, respectively. For the Z2 × J11 cross, the corresponding values were 10 and 20 PCs. For 29 fungal OTUs and 10 bacterial OTUs out of the most abundant 100 OTUs, genetic variance (VT) was significantly greater than VE for the L1 × Z49 cross; the corresponding values for the Z2 × J11 cross were 24 and one. The estimated heritability was mostly in the range of 40% to 60%. These results suggested the existence of genetic control of polygenic nature for specific components of rhizosphere microbiome in cotton. KEY POINTS: • F2 offspring cotton plants differed significantly from parents in rhizosphere microbial diversity. • Specific rhizosphere components are likely to be genetically controlled by plants. • Common PCs and specific microbial groups are significant genetic components between the two crosses.

Microbacterium rhizophilus sp. nov., an indole acetic acid-producing actinobacterium isolated from rhizosphere soil.

A novel gram-stain-positive, short rod, aerobic, non-motile and non-spore-forming actinobacterial strain, designated GXG1230T was isolated from the rhizosphere soil of a coastal mangrove forest in Beihai city, Guangxi Zhuang Autonomous Region, PR China. Phylogenetic analysis based on 16S rRNA gene sequences revealed that strain GXG1230T was affiliated with the genus Microbacterium. Additionally, it demonstrated a high degree of similarity to Microbacterium paludicola US15T (97.9%) and Microbacterium marinilacus YM11-607T (97.3%). Chemotaxonomic characteristics showed that the whole-cell sugars were glucose, xylose, rhamnose and galactose. Menaquinones MK-11 and MK-12 were detected as respiratory quinones. Lysine was found in the peptidoglycan hydrolysate and the polar lipids were diphosphatidylglycerol, one phospholipid and two unidentified glycolipid. The major fatty acids were anteiso-C15:0, iso-C16:0 and anteiso-C17:0. The strain GXG1230T exhibited a genomic DNA G + C content of 71.7%. Furthermore, the average nucleotide identity values of GXG1230T with the reference strains were 75.4% and 81.9%, respectively, while the digital DNA-DNA hybridization values were 20.1% and 25.0%. Based on physiological, chemotaxonomic and phylogenetic information, strain GXG1230T is considered to represent a novel species of the genus Microbacterium, for which the name Microbacterium rhizophilus sp.nov is proposed, with GXG1230T (= MCCC 1K09302T = KCTC 59252T) as the type strain.

Terrihabitans rhizophilus sp. nov., isolated from the rhizosphere soil of plant in temperate semi-arid steppe.

A bacterial strain PJ23T was isolated from the rhizosphere soil of Elymus dahuricus Turcz. sampled from a temperate semi-arid steppe in the northern of Inner Mongolia Autonomous Region, China. The strain is Gram-stain-negative, aerobic, light-pink, short rod-shaped, and non-spore-forming. Cell growth could be observed at 4-29℃ (optimal at 24℃), pH 6.0-8.6 (optimal at 8.0) and in the presence of 0-5.0% (w/v) NaCl (optimal at 2.5%). The major cellular fatty acids of strain PJ23T were Summed feature 8 (C18:1 ω6c and/or C18:1 ω7c) (39.42%) and C16:0 (9.60%). The polar lipids were phosphatidylcholine, two unidentified glycolipids, one unidentified aminophospholipid, and two other unidentified polar lipids. The major respiratory quinone was ubiquinone-10. Phylogeny analysis based on 16S rRNA gene sequences retrieved from the genomes showed that, the strain was closely related to the species Terrihabitans soli IZ6T and Flaviflagellibacter deserti SYSU D60017T, with the sequence similarities of 96.79% and 96.15%, respectively. The G + C content was 65.23 mol% calculated on draft genome sequencing. Between the strains PJ23T and Terrihabitans soli IZ6T, the average nucleotide identity (ANI), amino acid identity (AAI) and digital DNA-DNA hybridization (dDDH) was 73.39%,71.12% and 15.7%, these values were lower than the proposed and generally accepted species boundaries of ANI, AAI and dDDH, respectively. Based on phenotypic, chemotaxonomic, and phylogenetic characteristics, strain PJ23T represents a novel species of Terrihabitans, for which the name Terrihabitans rhizophilus sp. nov. is proposed. The type strain is PJ23T (= KCTC 92977 T = CGMCC 1.61577 T).

Oerskovia flava sp. nov., a deoxynivalenol (DON)-degrading actinomycete isolated from the rhizosphere soil of long-term continuous cropping cucumber.

The deoxynivalenol (DON)-degrading bacterium JB1-3-2 T was isolated from a rhizosphere soil sample of cucumber collected from a greenhouse located in Zhenjiang, Eastern China. The JB1-3-2 T strain is a Gram-stain-positive, nonmotile and round actinomycete. Growth was observed at temperatures between 15 and 40 ℃ (optimum, 35 ℃), in the presence of 15% (w/v) NaCl (optimum, 3%), and at pH 3 and 11 (optimum, 7). The major cellular fatty acids identified were anteiso-C15:0, iso-C16:0 and anteiso-C17:0. Genome sequencing revealed a genome size of 4.11 Mb and a DNA G + C content of 72.5 mol%. Phylogenetic analysis based on 16S rRNA gene sequences indicated that the JB1-3-2 T strain was most closely related to type strains of the Oerskovia species, with the highest sequence similarity to Oerskovia turbata NRRL B-8019 T (98.2%), and shared 98.1% sequence identity with other valid type strains of this genus. Digital DNA‒DNA hybridization (dDDH) and average nucleotide identity (ANI) showed 21.8-22.2% and 77.2-77.3% relatedness, respectively, between JB1-3-2 T and type strains of the genus Oerskovia. Based on genotypic, phylogenetic, chemotaxonomic, physiological and biochemical characterization, Oerskovia flava, a novel species in the genus Oerskovia, was proposed, and the type strain was JB1-3-2 T (= CGMCC 1.18555 T = JCM 35248 T). Additionally, this novel strain has a DON degradation ability that other species in the genus Oerskovia do not possess, and glutathione-S-transferase was speculated to be the key enzyme for strain JB1-3-2 T to degrade DON.

Multi-omics analyses reveal the responses of wheat (Triticum aestivum L.) and rhizosphere bacterial community to nano(micro)plastics stress.

The pervasive existence of nanoplastics (NPs) and microplastics (MPs) in soil has become a worldwide environmental concern. N/MPs exist in the environment in a variety of forms, sizes, and concentrations, while multi-omics studies on the comprehensive impact of N/MPs with different properties (e.g. type and size) on plants remain limited. Therefore, this study utilized multi-omics analysis methods to investigate the effects of three common polymers [polyethylene-NPs (PE-NPs, 50 nm), PE-MPs (PE-MPs, 10 µm), and polystyrene-MPs (PS-MPs, 10 µm)] on the growth and stress response of wheat, as well as the rhizosphere microbial community at two concentrations (0.05 and 0.5 g/kg). PS and PE exhibited different effects for the same particle size and concentration. PE-NPs had the most severe stress effects, resulting in reduced rhizosphere bacteria diversity, plant biomass, and antioxidant enzyme activity while increasing beneficial bacteria richness. N/MPs altered the expression of nitrogen-, phosphorus-, and sulfur-related functional genes in rhizosphere bacteria, thereby affecting photosynthesis, as well as metabolite and gene levels in wheat leaves. Partial least squares pathway models (PLSPMs) indicated that concentration, size, and type play important roles in the impact of N/MPs on the plant ecological environment, which could have essential implications for assessing the environmental risk of N/MPs.

Assembly patterns and key taxa of bacterial communities in the rhizosphere soil of moso bamboo (Phyllostachys pubescens) under different Cd and Pb pollution.

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

To date, little is known about the bacterial communities in the rhizosphere of moso bamboo under Cd and Pb multiple stresses. This study investigated the assembly patterns and key taxa of rhizospheric bacterial communities of moso bamboo in Cd/Pb polluted and unpolluted soils. It was found that the bacterial community structure in bamboo rhizosphere is easily influenced by soil chemical environment, such as fertilities and heavy metals. The key bacterial taxa identified here could be target microbe in future microbe-assistant phytoremediation.

Soil Microbial Community Involved in Nitrogen Cycling in Rice Fields Treated with Antiozonant under Ambient Ozone.

Ethylenediurea (EDU) can effectively mitigate the crop yield loss caused by ozone (O3), a major, phytotoxic air pollutant. However, the relevant mechanisms are poorly understood, and the effect of EDU on soil ecosystems has not been comprehensively examined. In this study, a hybrid rice variety (Shenyou 63) was cultivated under ambient O3 and sprayed with 450 ppm EDU or water every 10 days. Real time quantitative polymerase chain reaction (RT-qPCR) showed that EDU had no significant effect on the microbial abundance in either rhizospheric or bulk soils. By applying both metagenomic sequencing and the direct assembly of nitrogen (N)-cycling genes, EDU was found to decrease the abundance of functional genes related to nitrification and denitrification processes. Moreover, EDU increased the abundance of genes involved in N-fixing. Although the abundance of some functional genes did not change significantly, nonmetric multidimensional scaling (NMDS) and a principal coordinates analysis (PCoA) suggested that the microbial community structure involved in N cycling was altered by EDU. The relative abundances of nifH-and norB-harboring microbial genera in the rhizosphere responded differently to EDU, suggesting the existence of functional redundancy, which may play a key role in sustaining microbially mediated N-cycling under ambient O3. IMPORTANCE Ethylenediurea (EDU) is hitherto the most efficient phytoprotectant agent against O3 stress. However, the underlying biological mechanisms of its mode of action are not clear, and the effects of EDU on the environment are still unknown, limiting its large-scale application in agriculture. Due to its sensitivity to environmental changes, the microbial community can be used as an indicator to assess the environmental impacts of agricultural practices on soil quality. This study aimed to unravel the effects of EDU spray on the abundance, community structure, and ecological functions of microbial communities in the rhizosphere of rice plants. Our study provides a deep insight into the impact of EDU spray on microbial-mediated N cycling and the structure of N-cycling microbial communities. Our findings help to elucidate the mode of action of EDU in alleviating O3 stress in crops from the perspective of regulating the structure and function of the rhizospheric soil microbial community.

Isolation and in-vitro characterization of extracellular phytase producing bacterial isolates for potential application in poultry feed.

BACKGROUND: Phytase catalyses the breakdown of complex organic forms of phosphorous into simpler forms by sequential hydrolysis of phosphate ester bonds to liberate the inorganic phosphate. Supplementation of feeds with bacterial phytase therefore could enhance the bioavailability of phosphorus and micronutrients. Hence, the aim of this study was to isolate and characterize phytase producing bacteria from rhizosphere soil, fresh poultry excreta, and cattle shed to evaluate their potential in improving poultry feeds. Phytase producing bacteria were isolated using wheat bran extract medium. RESULTS: A total of 169 bacterial isolates were purified and screened for phytase activity. Out of these, 36 were confirmed as positive for phytase enzyme activity. The bacterial isolates were identified by cultural, morphological, and biochemical features. The isolates were also identified by using 16 S rRNA gene sequencing. The bacterial isolates (RS1, RS8, RS10 and RS15) were provided with gene bank database accession numbers of MZ407562, MZ407563, MZ407564 and MZ407565 respectively. All isolates increased phytase production when cultured in wheat bran extract medium (pH 6) supplemented with 1% (wt/v) galactose and 1% (wt/v) ammonium sulphate incubated at 50oC for 72 h. Proximate composition analysis after supplementation of phytase showed that phytase supplementation improved bioavailability of phosphorus, calcium, potassium and sodium in poultry feed. CONCLUSIONS: Overall, this study showed that the nutritional value of poultry feed can be improved using microbial phytase enzyme which reduces the cost of supplementation with inorganic phosphate.

Actinophytocola gossypii sp. nov. and Streptomyces gossypii sp. nov., two novel actinomycetes isolated from rhizosphere soil of cotton.

Two Gram-positive, aerobic and non-motile actinomycetes, designated S1-96T and N2-109T, were isolated from soils collected from a cotton field. They are described as representing two novel species of genera Actinophytocola and Streptomyces through a polyphasic approach. Analysis of 16S rRNA gene sequences revealed that strains S1-96T and N2-109T showed highest similarity to Actinophytocola xinjiangensis CGMCC 4.4663T (99.10 %) and Streptomyces iconiensis BNT558T (98.21 %), respectively. Phylogenetic analyses based on 16S rRNA and core genes confirmed the close relationships of these strains. Genomic analyses further supported the novel taxonomic delimitation of these two species based on digital DNA-DNA hybridization and average nucleotide identity. Strains S1-96T and N2-109T contained MK-9(H4) and MK-9(H6) as the most abundant menaquinone, respectively. High abundances of iso-fatty acids were detected in both strains, which was similar to their close relatives. Physiological and polar lipid analyses also revealed differences between these strains and their phylogenetic neighbours, supporting their taxonomic delimitation as novel species. The names Actinophytocola gossypii sp. nov. (type strain S1-96T=JCM 34412T=CGMCC 4.7707T) and Streptomyces gossypii sp. nov. (type strain N2-109T=JCM 34628T=CGMCC 4.7717T) are proposed.

Luteimonas suaedae sp. nov., a novel bacterium isolated from rhizosphere of Suaeda aralocaspica (Bunge) Freitag & Schütze.

Light yellowish-white colonies of a bacterial strain, designated LNNU 24178T, were isolated from the rhizosphere soil of halophyte Suaeda aralocaspica (Bunge) Freitag and Schütze grown at Shihezi district, Xinjiang, PR China. Cells were Gram-stain-negative, non-flagellum-forming, rod-shaped and non-motile. The results of phylogenetic analysis based on the 16S rRNA gene sequence indicated that LNNU 24178T represented a member of the genus Luteimonas and shared the highest sequence similarity with Luteimonas yindakuii CGMCC 1.13927T (97.1 %) and lower sequence similarity (< 97.0 %) to other known species. The genomic DNA G+C content of LNNU 24178T was 68.8 %. The average nucleotide identity (ANI) values between LNNU 24178T and Luteimonas yindakuii CGMCC 1.13927T, Luteimonas mephitis DSM 12574T, Luteimonas arsenica 26-35T and Luteimonas huabeiensis HB2T were 78.7, 78.6, 78.4 and 80.0 %, respectively. The digital DNA-DNA hybridisation (dDDH) values between LNNU 24178T and L. yindakuii CGMCC 1.13927T, L. mephitis DSM 12574T, L. arsenica 26-35T and L. huabeiensis HB2T were 22.0, 22.3, 22.2 and 23.5 %, respectively. The respiratory quinone detected in LNNU 24178T was ubiquinone-8 (Q-8). The major fatty acids (> 5.0 %) of LNNU 24178T were identified as iso-C15 : 0 (33.9 %), iso-C17 : 0 (8.7 %), iso-C11 : 0 (6.2 %), iso-C16 : 0 (5.7 %), C16 : 0 (5.3 %) and summed feature 9 (iso-C17 : 1ω9c/10-methyl C16 : 0) (21.1 %). The major polar lipids of LNNU 24178T were diphosphatidylglycerol (DPG), phosphatidylglycerol (PG), phosphatidylethanolamine (PE), one unidentified phospholipid (PL), one unidentified glycolipid (GL) and three unidentified lipids. According to the data obtained from phenotypic, chemotaxonomic and phylogenetic analyses, strain LNNU 24178T represents a novel species of the genus Luteimonas, for which the name Luteimonas suaedae sp. nov. is proposed, with LNNU 24178T (= CGMCC 1.17331T= KCTC 62251T) as the type strain.