An Unknown Non-denitrifier Bacterium Isolated from Soil Actively Reduces Nitrous Oxide under High pH Conditions

Dominant role of water-extractable soil chemicals in modulating N₂O emissions relative to soil bacteriome

Soil nitrous oxide (N₂O) emissions are influenced both by soil chemical properties and microbiome composition; however, their relative contributions remain unclear. We used soil-water extracts (SW), and cell extracts (bacteriomes) from two contrasting soils, black soil (BS) and fluvo-aquic soil (FS), to evaluate how water-extractable soil chemicals and bacteriomes directly impact N₂O emissions, as well as how SW influences bacteriome composition. Results show that SW chemistry, particularly pH, plays a dominant role in regulating denitrification dynamics, while bacteriome effects are less significant. In native BS water extract (BSW, pH 6.5), cell extract from BS (BB bacteriomes) exhibited high N₂O emissions (N₂O index = 0.669), but their denitrification efficiency improved in FS water extract (FSW, pH 8.2), reducing the N₂O index to 0.0491. Conversely, cell extract from FS (FB bacteriomes) in native FSW (pH 8.2) demonstrated efficient denitrification (N₂O index = 0.006), but exposure to BSW increased N₂O emissions (∼ 100 µmol vial⁻¹, N₂O index = 0.295). Bacterial community analysis revealed that high pH fostered diverse denitrifiers, including napA-harboring Pseudoxanthomonas and Lysobacter, and nosZ Clade II Chitinophaga, which are linked to N₂O reduction. In contrast, low pH favored narG-harboring incomplete denitrifiers like Klebsiella and Enterobacter. In the BB bacteriome, BSW promoted Rhodanobacter, which hindered complete denitrification, while FSW enriched complete denitrifiers like Cupriavidus and Ensifer. Conversely, BSW negatively impacted the enrichment of complete denitrifier Acidovorax in the FB bacteriome. This study contributes to the growing evidence of the critical roles of soil physicochemical properties and bacteriome composition in determining N₂O fluxes from agricultural soils.

A novel plant growth-promoting rhizobacterium, Rhizosphaericola mali gen. nov., sp. nov., isolated from healthy apple tree soil

The rhizosphere microbial community is closely associated with plant disease by regulating plant growth, agricultural production, nutrient availability, plant hormone and adaptation to environmental changes. Therefore, it is very important to identify the rhizosphere microbes around plant roots and understand their functions. While studying the differences between the rhizosphere microbiota of healthy and diseased apple trees to find the cause of apple tree disease, we isolated a novel strain, designated as B3-10T, from the rhizosphere soil of a healthy apple tree. The genome relatedness indices between strain B3-10T and other type species of family Chitinophagaceae were in the ranges of 62.4-67.0% for ANI, 18.6-32.1% for dDDH, and 39.0-56.6% for AAI, which were significantly below the cut‑off values for the species delineation, indicating that strain B3-10T could be considered to represent a novel genus in family Chitinophagaceae. Interestingly, the complete genome of strain B3-10T contained a number of genes encoding ACC-deaminase, siderophore production, and acetoin production contributing to plant-beneficial functions. Furthermore, strain B3-10T was found to significantly promote the growth of shoots and roots of the Nicotiana benthamiana, which is widely used as a good model for plant biology, demonstrating that strain B3-10T, a rhizosphere microbe of healthy apple trees, has the potential to promote growth and reduce disease. The phenotypic, chemotaxonomic, phylogenetic, genomic, and physiological properties of this plant growth-promoting (rhizo)bacterium, strain B3-10T supported the proposal of a novel genus in the family Chitinophagaceae, for which the name Rhizosphaericola mali gen. nov., sp. nov. (= KCTC 72123T = NBRC 114178T).

Existence of antibiotic pollutant in agricultural soil: Exploring the correlation between microbiome and pea yield

Due to sewage irrigation, manure fertilizer application or other agricultural activities, antibiotics have been introduced into farmland as an emerging contaminant, existing with other agrochemicals. However, the potential influences of antibiotics on the efficiency of agrochemicals and crops health are still unclear. In this work, the effect of antibiotics on fertilization efficiency and pea yield was evaluated, and the mechanism was explored in view of soil microbiome. Nitrogen utilization and pea yield were decreased by antibiotics. In specific, the weight of seeds decreased 9.5 % by 5 mg/kg antibiotics and decreased 25.1 % by 50 mg/kg antibiotics. For N nutrient in pea, antibiotics resulted in 62.5 %-63.7 % decrease in amino acid content and 8.3 %-35.3 % decrease in inorganic-N content. Further research showed that antibiotics interfered with N cycle in soil, inhibiting urea decomposition and denitrification process by reducing function genes ureC, nirK and norB in soil, thus decreasing N availability. Meanwhile, antibiotics destroyed the enzyme function in N assimilation. This work evaluated the environmental risk of antibiotics from fertilization efficiency and N utilization in crop. Antibiotics could not only affect N cycle, limiting the decomposition of N fertilizer, but also affect N utilization in plants, thus affecting the yield and even the quality of leguminous crops.

Nitrous Oxide Emission in Response to pH from Degrading Palsa Mire Peat Due to Permafrost Thawing

N₂O, a greenhouse gas, is increasingly emitted from degrading permafrost mounds of palsa mires because of the global warming effects on microbial activity. In the present study, we hypothesized that N₂O emission could be affected by a change in pH conditions because the collapse of acidic palsa mounds (pH 3.4-4.6) may result in contact with minerogenic ground water (pH 4.8-6.3), thereby increasing the pH. We compared the effects of pH change on N₂O emission from cultures inoculated with peat suspensions. Peat samples were collected on a transect from a still intact high part to the collapsing edge of a degrading palsa mound in northwestern Finland, assuming the microbial communities could be different. We adjusted the pH of peat suspensions prepared from a collapsing palsa mound and compared the N₂O emission in a pH gradient from 4.5 to 8.5. The collapsing edge had the highest N₂O emission from the peat suspensions among all points on the transect under natural acidic conditions (pH 4.5). The N₂O emission was reduced with a moderate rise in pH (pH 5.0-6.0) by approximately 85% compared with natural acidic level (pH 4.5). The bacterial communities in acidic cultures differed considerably from those in alkaline cultures. When pH was adjusted to alkaline conditions, N₂O-emitting bacteria different from those present in acidic conditions appeared to emit N₂O. The bacterial communities could be characterized by changing pH conditions after thawing and collapse of permafrost have contrasting impacts on N₂O production that calls for further attention in future studies.

Identification of a phosphorus-solubilizing Tsukamurella tyrosinosolvens strain and its effect on the bacterial diversity of the rhizosphere soil of peanuts growth-promoting

Phosphate solubilizing microorganisms widely exist in plant rhizosphere soil, but report about the P solubilization and multiple growth-promoting properties of rare actinomycetes are scarce. In this paper, a phosphate solubilizing Tsukamurella tyrosinosolvens P9 strain was isolated from the rhizosphere soil of tea plants. Phosphorus-dissolving abilities of this strain were different under different carbon and nitrogen sources, the soluble phosphorus content was 442.41 mg/L with glucose and potassium nitrate as nutrient sources. The secretion of various organic acids, such as lactic acid, maleic acid, oxalic acid, etc., was the main mechanism for P solubilization and pH value in culture was very significant negative correlation with soluble P content. In addition, this strain had multiple growth-promoting characteristics with 37.26 μg/mL of IAA and 72.01% of siderophore relative content. Under pot experiments, P9 strain improved obviously the growth of peanut seedlings. The bacterial communities of peanut rhizoshpere soil were assessed after inoculated with P9 strain. It showed that there was no significant difference in alpha-diversity indices between the inoculation and control groups, but the P9 treatment group changed the composition of bacterial communities, which increased the relative abundance of beneficial and functional microbes, which relative abundances of Chitinophagaceae at the family level, and of Flavihumibacter, Ramlibacter and Microvirga at the genus level, were all siginificant increased. Specially, Tsukamurella tyrosinosolvens were only detected in the rhizosphere of the inoculated group. This study not only founded growth-promoting properties of T. tyrosinosolvens P9 strain and its possible phosphate solublizing mechanism, but also expected to afford an excellent strain resource in biological fertilizers.