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Current Microbiology Jun 2024Two endophytic actinobacteria, strains MK5 and MK7, were isolated from the surface-sterilized root of Jasmine rice (Oryza sativa KDML 105). These strains were aerobic...
Two endophytic actinobacteria, strains MK5 and MK7, were isolated from the surface-sterilized root of Jasmine rice (Oryza sativa KDML 105). These strains were aerobic actinobacteria with a well-developed substrate and aerial mycelia that formed spiral spore chains. The type strains that shared the high 16S rRNA gene sequence similarity with both strains were Streptomyces naganishii NBRC 12892 (99.4%), "Streptomyces griseicoloratus" TRM S81-3 (99.2%), and Streptomyces spiralis NBRC 14215 (98.9%). Strains MK5 and MK7 are the same species sharing a digital DNA-DNA hybridization (dDDH) value of 95.3% and a 16S rRNA gene sequence similarity of 100%. Chemotaxonomic data confirmed the affiliation of strains MK5 and MK7 to the genus Streptomyces. Strains MK5 and MK7 contained MK-9(H) as a major menaquinone; the whole-cell sugar of both strains was galactose and glucose. The strain MK5 shared 93.4% average nucleotide identity (ANI)-Blast, 95.5% ANI-MUMmer, 93% average amino acid identity, and 61.3% dDDH with S. spiralis NBRC 14215. The polyphasic approach confirmed that strain MK5 represents a novel species, and the name Streptomyces mahasarakhamensis sp. nov. is proposed. The type strain is MK5 (= TBRC 17754 = NRRL B-65683). Genome mining, using an in silico approach and searching biosynthesis gene clusters of strains MK5 and MK7, revealed that the genomes contained genes encoding proteins relating to plant growth promotion, bioactive compounds, and beneficial enzymes. Strains MK5 and MK7 could produce indole acetic acid and solubilize phosphate in vitro.
Topics: Oryza; Streptomyces; Phylogeny; RNA, Ribosomal, 16S; Endophytes; DNA, Bacterial; Plant Roots; Plant Growth Regulators; Vitamin K 2; Bacterial Typing Techniques; Sequence Analysis, DNA; Nucleic Acid Hybridization; Fatty Acids; Base Composition
PubMed: 38874598
DOI: 10.1007/s00284-024-03747-0 -
The New Phytologist Jun 2024Intercropping leads to different plant roots directly influencing belowground processes and has gained interest for its promotion of increased crop yields and resource...
Intercropping leads to different plant roots directly influencing belowground processes and has gained interest for its promotion of increased crop yields and resource utilization. However, the precise mechanisms through which the interactions between rhizosphere metabolites and the microbiome contribute to plant production remain ambiguous, thus impeding the understanding of the yield-enhancing advantages of intercropping. This study conducted field experiments (initiated in 2013) and pot experiments, coupled with multi-omics analysis, to investigate plant-metabolite-microbiome interactions in the rhizosphere of maize. Field-based data revealed significant differences in metabolite and microbiome profiles between the rhizosphere soils of maize monoculture and intercropping. In particular, intercropping soils exhibited higher microbial diversity and metabolite chemodiversity. The chemodiversity and composition of rhizosphere metabolites were significantly related to the diversity, community composition, and network complexity of soil microbiomes, and this relationship further impacted plant nutrient uptake. Pot-based findings demonstrated that the exogenous application of a metabolic mixture comprising key components enriched by intercropping (soyasapogenol B, 6-hydroxynicotinic acid, lycorine, shikimic acid, and phosphocreatine) significantly enhanced root activity, nutrient content, and biomass of maize in natural soil, but not in sterilized soil. Overall, this study emphasized the significance of rhizosphere metabolite-microbe interactions in enhancing yields in intercropping systems. It can provide new insights into rhizosphere controls within intensive agroecosystems, aiming to enhance crop production and ecosystem services.
PubMed: 38874414
DOI: 10.1111/nph.19906 -
The New Phytologist Jun 2024Wood is resulted from the radial growth paced by the division and differentiation of vascular cambium cells in woody plants, and phytohormones play important roles in...
Wood is resulted from the radial growth paced by the division and differentiation of vascular cambium cells in woody plants, and phytohormones play important roles in cambium activity. Here, we identified that PagJAZ5, a key negative regulator of jasmonate (JA) signaling, plays important roles in enhancing cambium cell division and differentiation by mediating cytokinin signaling in poplar 84K (Populus alba × Populus glandulosa). PagJAZ5 is preferentially expressed in developing phloem and cambium, weakly in developing xylem cells. Overexpression (OE) of PagJAZ5m (insensitive to JA) increased cambium activity and xylem differentiation, while jaz mutants showed opposite results. Transcriptome analyses revealed that cytokinin oxidase/dehydrogenase (CKXs) and type-A response regulators (RRs) were downregulated in PagJAZ5m OE plants. The bioactive cytokinins were significantly increased in PagJAZ5m overexpressing plants and decreased in jaz5 mutants, compared with that in 84K plants. The PagJAZ5 directly interact with PagMYC2a/b and PagWOX4b. Further, we found that the PagRR5 is regulated by PagMYC2a and PagWOX4b and involved in the regulation of xylem development. Our results showed that PagJAZ5 can increase cambium activity and promote xylem differentiation through modulating cytokinin level and type-A RR during wood formation in poplar.
PubMed: 38874377
DOI: 10.1111/nph.19912 -
The New Phytologist Jun 2024The phytohormone abscisic acid (ABA) functions in the control of plant stress responses, particularly in drought stress. A significant mechanism in attenuating and...
The phytohormone abscisic acid (ABA) functions in the control of plant stress responses, particularly in drought stress. A significant mechanism in attenuating and terminating ABA signals involves regulated protein turnover, with certain ABA receptors, despite their main presence in the cytosol and nucleus, subjected to vacuolar degradation via the Endosomal Sorting Complex Required for Transport (ESCRT) machinery. Collectively our findings show that discrete TOM1-LIKE (TOL) proteins, which are functional ESCRT-0 complex substitutes in plants, affect the trafficking for degradation of core components of the ABA signaling and transport machinery. TOL2,3,5 and 6 modulate ABA signaling where they function additively in degradation of ubiquitinated ABA receptors and transporters. TOLs colocalize with their cargo in different endocytic compartments in the root epidermis and in guard cells of stomata, where they potentially function in ABA-controlled stomatal aperture. Although the tol2/3/5/6 quadruple mutant plant line is significantly more drought-tolerant and has a higher ABA sensitivity than control plant lines, it has no obvious growth or development phenotype under standard conditions, making the TOL genes ideal candidates for engineering to improved plant performance.
PubMed: 38874374
DOI: 10.1111/nph.19904 -
The New Phytologist Jun 2024A few Capsicum (pepper) species produce yellow-colored floral nectar, but the chemical identity and biological function of the yellow pigment are unknown. A combination...
A few Capsicum (pepper) species produce yellow-colored floral nectar, but the chemical identity and biological function of the yellow pigment are unknown. A combination of analytical biochemistry techniques was used to identify the pigment that gives Capsicum baccatum and Capsicum pubescens nectars their yellow color. Microbial growth assays, visual modeling, and honey bee preference tests for artificial nectars containing riboflavin were used to assess potential biological roles for the nectar pigment. High concentrations of riboflavin (vitamin B) give the nectars their intense yellow color. Nectars containing riboflavin generate reactive oxygen species when exposed to light and reduce microbial growth. Visual modeling also indicates that the yellow color is highly conspicuous to bees within the context of the flower. Lastly, field experiments demonstrate that honey bees prefer artificial nectars containing riboflavin. Some Capsicum nectars contain a yellow-colored vitamin that appears to play roles in (1) limiting microbial growth, (2) the visual attraction of bees, and (3) as a reward to nectar-feeding flower visitors (potential pollinators), which is especially interesting since riboflavin is an essential nutrient for brood rearing in insects. These results cumulatively suggest that the riboflavin found in some Capsicum nectars has several functions.
PubMed: 38874372
DOI: 10.1111/nph.19886 -
The New Phytologist Jun 2024Branch number is one of the most important agronomic traits of fruit trees such as peach. Little is known about how LncRNA and/or miRNA modules regulate branching...
Branch number is one of the most important agronomic traits of fruit trees such as peach. Little is known about how LncRNA and/or miRNA modules regulate branching through transcription factors. Here, we used molecular and genetic tools to clarify the molecular mechanisms underlying brassinosteroid (BR) altering plant branching. We found that the number of sylleptic branch and BR content in pillar peach ('Zhaoshouhong') was lower than those of standard type ('Okubo'), and exogenous BR application could significantly promote branching. PpTCP4 expressed great differentially comparing 'Zhaoshouhong' with 'Okubo'. PpTCP4 could directly bind to DWARF2 (PpD2) and inhibited its expression. PpD2 was the only one differentially expressed key gene in the path of BR biosynthesis. At the same time, PpTCP4 was identified as a target of miR6288b-3p. LncRNA1 could act as the endogenous target mimic of miR6288b-3p and repress expression of miR6288b-3p. Three deletions and five SNP sites of lncRNA1 promoter were found in 'Zhaoshouhong', which was an important cause of different mRNA level of PpTCP4 and BR content. Moreover, overexpressed PpTCP4 significantly inhibited branching. A novel mechanism in which the lncRNA1-miR6288b-3p-PpTCP4-PpD2 module regulates peach branching number was proposed.
PubMed: 38872462
DOI: 10.1111/nph.19903 -
Methods in Molecular Biology (Clifton,... 2024Photorespiration, an essential metabolic component, is a classic example of interactions between the intracellular compartments of a plant cell: the chloroplast,...
Photorespiration, an essential metabolic component, is a classic example of interactions between the intracellular compartments of a plant cell: the chloroplast, peroxisome, mitochondria, and cytoplasm. The photorespiratory pathway is often modulated by abiotic stress and is considered an adaptive response. Monitoring the patterns of key enzymes located in different subcellular components would be an ideal approach to assessing the modulation of the photorespiratory metabolism under abiotic stress. This chapter describes the procedures for assaying several individual enzyme activities of key photorespiratory enzymes and evaluating their response to oxidative/photooxidative stress. It is essential to ascertain the presence of stress in the experimental material. Therefore, procedures for typical abiotic stress induction in leaves by highlighting without or with menadione (an oxidant that targets mitochondria) are also included.
Topics: Plant Leaves; Stress, Physiological; Photosynthesis; Chloroplasts; Oxidative Stress; Enzyme Assays; Cell Respiration; Vitamin K 3; Arabidopsis; Light
PubMed: 38869793
DOI: 10.1007/978-1-0716-3973-3_10 -
International Journal of Systematic and... Jun 2024A Gram-stain-positive, aerobic bacterium, designated as YPD9-1, was isolated from the gut contents of a spotty belly greenling, , collected near Dokdo island, South...
A Gram-stain-positive, aerobic bacterium, designated as YPD9-1, was isolated from the gut contents of a spotty belly greenling, , collected near Dokdo island, South Korea. The rod-shaped cells were oxidase-positive, and catalase-negative. The major cellular fatty acids were anteiso-C, iso-C, C, iso-C and iso-C. The major polar lipids were diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine and two unidentified lipids. The DNA G+C content was 47.6 mol% and the predominant respiratory quinone was menaquinone MK-7. The 16S rRNA gene sequence of YPD9-1 showed low sequence similarities to species of the genus , Gsoil 1138 (97.21 % of sequence similarity), CJ25 (97.12 %) and JJ-42 (96.89 %). The results of phylogenetic analysis based on 16S rRNA gene sequences indicated that YPD9-1 formed a distinct branch among other species of the genus . The digital DNA-DNA hybridisation, average nucleotide identity, and average amino acid identity values between YPD9-1 and the related species were in the ranges of 15.3-16.2 %, 74.1-78.4 %, and 71.1-71.9 %, respectively, which are below the species cutoff values. On the basis of the results of the polyphasic analysis, we conclude that strain YPD9-1 represents a novel species of the genus , for which the name sp. nov. is proposed. The type strain of is YPD9-1 (=KCTC 43424 =LMG 32988).
Topics: RNA, Ribosomal, 16S; Base Composition; Phylogeny; DNA, Bacterial; Republic of Korea; Fatty Acids; Paenibacillus; Bacterial Typing Techniques; Sequence Analysis, DNA; Vitamin K 2; Animals; Nucleic Acid Hybridization; Phospholipids
PubMed: 38869487
DOI: 10.1099/ijsem.0.006419 -
The New Phytologist Jun 2024
PubMed: 38867470
DOI: 10.1111/nph.19909 -
International Journal of Systematic and... Jun 2024A Gram-stain-negative, aerobic, non-spore-forming, nonmotile, rod-shaped, and yellow-pigmented bacterium, designated strain JXAS1, was isolated from a freshwater sample...
A Gram-stain-negative, aerobic, non-spore-forming, nonmotile, rod-shaped, and yellow-pigmented bacterium, designated strain JXAS1, was isolated from a freshwater sample collected from Poyang Lake in China. Phylogenetic analysis based on 16S rRNA gene sequence revealed that the isolate belonged to the genus , being closest to DSM 6368 (98.61 %). The genome size of strain JXAS1 was 4.66 Mb with DNA G+C content 35.7 mol%. The average nucleotide identity and DNA-DNA hybridization values between strain JXAS1 and its closest relatives were below the threshold values of 95 and 70 %, respectively. The strain contained menaquinone 6 (MK-6) as the predominant menaquinone and the major polar lipids were phosphatidylethanolamine, one unidentified glycolipid, and one unidentified polar lipid. The major fatty acids (>5 %) were iso-C, summed feature 3 (C 7 and/or C 6), C, iso-C 3OH, iso-C 3OH, and summed feature 9 (iso-C 9 and/or 10-methyl C). Based on phylogenetic, genotypic, and phenotypic evidence, the isolated strain represents a new species in the genus , and the name is proposed. The type strain is JXAS1 (=GDMCC 1.1378=KCTC 62719).
Topics: Flavobacterium; Lakes; Phylogeny; China; RNA, Ribosomal, 16S; Base Composition; Fatty Acids; Vitamin K 2; DNA, Bacterial; Bacterial Typing Techniques; Sequence Analysis, DNA; Nucleic Acid Hybridization; Phosphatidylethanolamines; Glycolipids; Phospholipids
PubMed: 38865183
DOI: 10.1099/ijsem.0.006416