Crosstalk between in situ root exudates and rhizobacteria to promote rice growth by selenium nanomaterials

Maximizing the potential of plant-microbe systems offers great opportunities to confront sustainability issues in agroecosystems. However, the dialog between root exudates and rhizobacteria remains largely unknown. As a novel nanofertilizer, nanomaterials (NMs) have significant potential to improve agricultural productivity due to their unique properties. Here, soil amendment with 0.1 mg·kg^-1 selenium (Se) NMs (30-50 nm) significantly promoted rice seedling growth. Differences in root exudates and rhizobacteria were evident. At an earlier time point (3^rd week), Se NMs increased the relative content of malic and citric acid by 15.4- and 8.1-fold, respectively. Meanwhile, the relative abundances of Streptomyces and Sphingomonas were increased by 164.6 % and 38.3 %, respectively. As the exposure time increased, succinic acid (40.5-fold) at the 4^th week and salicylic acid (4.7-fold) and indole-3-acetic (7.0-fold) at the 5^th week were enhanced, while Pseudomonas and Bacillus increased at the 4^th (112.3 % and 50.2 %) and 5^th weeks (190.8 % and 53.1 %), respectively. Further analysis indicated that (1) Se NMs directly enhanced the synthesis and secretion of malic and citric acids by upregulating their biosynthesis and transporter genes and then recruited Bacillus and Pseudomonas; (2) Se NMs upregulated the chemotaxis and flagellar genes of Sphingomonas for more interaction with rice plants, thereby promoting rice growth and stimulating root exudate secretion. This crosstalk of root exudates and rhizobacteria enhanced nutrient uptake, resulting in promoted rice growth. Our study offers insights into the crosstalk between root exudates and rhizobacteria by NMs and provides new insights into rhizosphere regulation in nano-enabled agriculture.

Sphingomonas psychrotolerans sp. nov., isolated from root surface of Leontopodium leontopodioides in the Tianshan Mountains, Xinjiang, China

A novel rod-shaped, Gram-stain-negative, aerobic bacterial strain, designated Cra20T, was isolated from the root surface of Leontopodium leontopodioides collected in the Tianshan Mountains, Xinjiang, PR China. Phylogenetic analysis based on 16S rRNA gene sequences, indicated that strain Cra20T was affiliated with the genus Sphingomonas , and was most closely related to Sphingomonas gei ZFGT-11T (99.0 %), Sphingomonas naasensis KIS18-15T (97.8%) and Sphingomonas kyeonggiensis THG-DT81T (97.2 %). The average nucleotide identity values between strain Cra20T, S. gei ZFGT-11T, S. naasensis KIS18-15T and S. kyeonggiensis THG-DT81T were 86.2, 84.2 and 78.2 %, respectively. The genomic DNA G+C content of strain Cra20T was 65.6 mol% (whole genome sequence), and Q-10 was the predominant ubiquinone. The major cellular fatty acids of strain Cra20T were summed feature 8 (comprising C18 : 1  ω6c and/or C18 : 1  ω7c, 67.3 %) and C14 : 0 2-OH (6.4 %). On the basis of genotypic, phenotypic and biochemical data, strain Cra20T is considered to represent a novel species of the genus Sphingomonas , for which the name Sphingomonas psychrotolerans sp. nov. is proposed. The type strain is Cra20T (=CGMCC 1.15510T=NBRC 112697T).

Long-Term Persistence of Arbuscular Mycorrhizal Fungi in the Rhizosphere and Bulk Soils of Non-host Brassica napus and Their Networks of Co-occurring Microbes

Arbuscular mycorrhizal fungi (AMF) are obligate plant symbionts that improve the nutrition and health of their host. Most, but not all the crops form a symbiosis with AMF. It is the case for canola (Brassica napus), an important crop in the Canadian Prairies that is known to not form this association. From 2008 to 2018, an experiment was replicated at three locations of the Canadian Prairies and it was used to assess the impact of canola on the community of AMF naturally occurring in three cropping systems, canola monoculture, or canola in two different rotation systems (2-years, canola-wheat and 3-years, barley-pea-canola). We sampled canola rhizosphere and bulk soils to: (i) determine diversity and community structure of AMF, we expected that canola will negatively impact AMF communities in function of its frequency in crop rotations and (ii) wanted to assess how these AMF communities interact with other fungi and bacteria. We detected 49 AMF amplicon sequence variants (ASVs) in canola rhizosphere and bulk soils, confirming the persistence of a diversified AMF community in canola-planted soil, even after 10 years of canola monoculture, which was unexpected considering that canola is among non-mycorrhizal plants. Network analysis revealed a broad range of potential interactions between canola-associated AMF and some fungal and bacterial taxa. We report for the first time that two AMF, Funneliformis mosseae and Rhizophagus iranicus, shared their bacterial cohort almost entirely in bulk soil. Our results suggest the existence of non-species-specific AMF-bacteria or AMF-fungi relationships that could benefit AMF in absence of host plants. The persistence of an AMF community in canola rhizosphere and bulk soils brings a new light on AMF ecology and leads to new perspectives for further studies about AMF and soil microbes interactions and AMF subsistence without mycotrophic host plants.

Sphingomonas montanisoli sp. nov., isolated from mountain soil

A soil bacterium, designated ZX9611T, was isolated from Taihang Mountain in Henan province, PR China. The strain was Gram-stain-negative and strictly aerobic. The cells were motile, rod-shaped and formed light pink-colored colonies. The 16S rRNA gene sequence of ZX9611T shared the highest similarities with those of Sphingomonas crocodyli CCP-7T (97.0%), Sphingomonas jatrophae S5-249T (96.6%) and Sphingomonas starnbergensis 382T (95.9%). Phylogenetic analyses based on 16S rRNA gene sequences demonstrated that ZX9611T clustered with S. crocodyli CCP-7T, S. jatrophae S5-249T and S. starnbergensis 382T. The average nucleotide identity (ANI) values between ZX9611T and two type strains ( S. crocodyli BCRC 81096T and S. jatrophae DSM 27345T) were 88.3 and 68.6% respectively. ZX9611T exhibited genome-sequence-based digital DNA–DNA hybridization (dDDH) values of 53.3 % and 15.3 %, compared with S. crocodyli BCRC 81096T and S . jatrophae DSM 27345T, respectively. ZX9611T had a genome size of 4.12 Mb and an average DNA G+C content of 64.8 %. ZX9611T had major fatty acids (>5 %) including summed feature 8 (C18 : 1  ω7c and/or C18 : 1  ω6c), C14 : 0 2-OH, C16 : 0 and summed feature 3 (C16 : 1  ω7c and/or C16 : 1  ω6c), and the major polyamine was sym-homospermidine. The only respiratory quinone was ubiquinone-10. The polar lipids were diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol, phosphatidylcholine and sphingoglycolipid. On the basis of phenotypic, chemotaxonomic and phylogenetic characteristics, strain ZX9611T represents a novel species of genus Sphingomonas, for which the name Sphingomonas montanisoli sp. nov. is proposed. The type strain is ZX9611T (=KCTC 72622T=CCTCC AB 2019350T).

Sphingomonas suaedae sp. nov., a chitin-degrading strain isolated from rhizosphere soil of Suaeda salsa

A Gram-stain-negative, aerobic, chitin-degrading, motile bacterial strain with a single polar flagellum, designated XS-10T, was isolated from saline soil sampled from the rhizosphere of Suaeda salsa, Tumd Right Banner, Inner Mongolia, PR China. Strain XS-10T grew at 10–40 °C (optimum, 35 °C), pH 5.0–9.0 (optimum, pH 8.0) and 0–12.5% NaCl (optimum 2.0 %). The phylogenetic analysis based on both the 16S rRNA gene and the phylogenomic tree revealed that strain XS-10T formed a clade with Sphingomonas turrisvirgatae MCT13T and Sphingomonas koreensis JSS-26T, sharing 98.4 and 97.5 % 16S rRNA gene similarities to S. koreensis JSS-26T and S. turrisvirgatae MCT13T, respectively. Spermidine and Q-10 were the major polyamine and the major respiratory quinone, respectively. The major polar lipids were diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol, sphingoglycolipid, two unidentified lipids and an unidentified aminophospholipid. The major fatty acids were summed feature 8 (C18 : 1  ω7c and/or C18 : 1  ω6c), C16 : 0 and C17 : 1  ω6c. The genome of strain XS-10T consisted of a 4 154 291 bp chromosome with a DNA G+C content of 65.5 mol%. The average nucleotide identity, average amino acid identity and digital DNA–DNA hybridization values of strain XS-10T with S. turrisvirgatae MCT13T and S. koreensis JSS-26T were 77.8 and 78.6 %, 75.9 and 76.3 %, and 22.0 and 22.9 %, respectively. Based on the phylogenetic, phenotypic, and genotypic characteristics, strain XS-10T is considered to represent a novel species of the genus Sphingomonas , for which the name Sphingomonas suaedae sp. nov. is proposed. The type strain is XS-10T (=CGMCC 1.17078T=JCM 33850T).

Sphingomonas paeninsulae sp. nov., isolated from soil sampled at Fildes Peninsula, Antarctica

Strain YZ-8^T, isolated from soil sampled at Fildes Peninsula, Antarctica, was found to be a Gram-stain-negative, yellow-pigmented, oxidase- and catalase-positive, non-motile, non-spore-forming, rod-shaped and aerobic bacterium. Strain YZ-8^T grewoptimally at pH 7.0 and 20 °C. Tolerance to NaCl was up to 0.3 % (w/v) with optimum growth in the absence of NaCl. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain YZ-8^T belonged to the family Sphingomonas. Strain YZ-8^T showed the highest sequence similarities to Sphingomonas molluscorum KMM 3882^T (94.4 %), Sphingomonas oligophenolica JCM 12082^T (94.4 %), Sphingomonas gotjawalisoli SN6-9^T (94.3 %) and Sphingomonas aquatica W1-2-1^T (94.3 %). The predominant respiratory isoprenoid quinone and polyamine components were identified as ubiquinone Q-10 and sym-homospermidine, respectively. In addition, carotenoid were also found. The polar lipid profile of the strain YZ-8^T was found to contain one phosphatidylethanolamine, an unidentified phospholipid, one diphosphatidylglycerol, one phosphatidylglycerol, two sphingophosphonolipids, one phosphatidylcholine and two unidentified alkali-stable lipids. The G+C content of the genomic DNA was determined to be 58.8 mol%. The main fatty acids were summed feature 8 (comprising C_18 : 1ω7c and/or C_18 : 1ω6c; 35.4 %), summed feature 3 (comprising C_16 : 1ω7c and/or C_16 : 1ω6c; 32.6 %) and C_14 : 0 2-OH (7.7 %). On the basis of the evidence presented in this study, a novel species of the genus Sphingomonas, Sphingomonaspaeninsulae sp. nov., is proposed, with the type strain YZ-8^T (=CCTCC AB 2017137^T=LMG 31027^T).

Impact of Artemisia absinthium hydrolate extracts with nematicidal activity on non-target soil organisms of different trophic levels

Natural pesticides are considered a good alternative to synthetic pesticides to reduce environmental impacts. However, biopesticides may have unknown effects on the environment, and can affect non-target organisms. In this study, the ecotoxicological effects of an aqueous extract (hydrolate) from Spanish populations of Artemisia absinthium (var. Candial) showing a promising biopesticide activity, were evaluated on non-target soil organisms from different trophic levels (natural microbial communities characterized through 16S rRNA gene sequencing, the earthworm Eisenia fetida and the plant Allium cepa). The hydrolate usually was considered as a by-product of the distillation to obtain essential oils. However, recently has been found to have nematicide properties. The hydrolate caused acute toxicity at values of LC₅₀ of 3.87% v/v for A. cepa and 0.07 mL/g for E. fetida. All the concentrations except for the most diluted (1% v/v) reduced the bacterial physiological activity compared to controls (LC₅₀ = 25.72% v/v after 24 h of exposure). The hydrolate also slightly altered the ability of the microbial community to degrade carbon substrates. These results indicate that the hydrolate from A. absinthium may affect the survival and metabolic abilities of key soil organisms.