Noviherbaspirillum humi sp. nov., isolated from soil

Effects of Water and Nitrogen on Growth, Rhizosphere Environment, and Microbial Community of Sophora alopecuroides: Their Interrelationship

The effective management of water and nitrogen is crucial in the artificial cultivation of medicinal plants. Sophora alopecuroides, a perennial herbaceous plant in the Fabaceae family, is extensively used in medicine, with alkaloids as its primary bioactive constituents. Nevertheless, there remains a significant knowledge gap regarding how rhizospheric microbial communities respond to varying water and nitrogen conditions and their intricate relationships with soil environments and the growth of S. alopecuroides. In this study, two-year-old S. alopecuroides were used in a two-factor, three-level water-nitrogen interaction experiment. The irrigation levels included W1 (30-35% of maximum water holding capacity), W2 (50-55%), and W3 (70-75%), while nitrogen levels comprised N1 (32 mg/kg), N2 (64 mg/kg), and N3 (128 mg/kg). The study assessed plant growth indicators, total alkaloid content, and rhizospheric soil physicochemical parameters of S. alopecuroides. High-throughput sequencing (16S rRNA and ITS) was employed to analyze variations in rhizospheric microbial community composition and structure. The results showed that Proteobacteria and Ascomycota are the predominant bacterial and fungal phyla in the rhizosphere microbial community of S. alopecuroides. The highest biomass and alkaloid accumulation of S. alopecuroides were observed under the N1W3 treatment (50% nitrogen application and 70-75% of maximum water holding capacity). Specifically, six bacterial genus-level biomarkers (TRA3_20, MND1, env_OPS_17, SBR1031, Haliangium, S0134_terrestrial_group) and six fungal genus-level biomarkers (Pseudeurotium, Rhizophagus, Patinella, Pseudeurotium, Patinella, Rhizophagus) were identified under the N1W3 treatment condition. In the partial least squares path modeling (PLS-PM), water and nitrogen treatments demonstrated markedly positive direct effects on soil physicochemical parameters (p < 0.01), while showing significant negative direct impacts on alkaloid accumulation and plant growth indicators (p < 0.05). Soil physicochemical parameters, in turn, significantly negatively affected the rhizosphere fungal community (p < 0.05). Additionally, the rhizosphere fungal community exhibited highly significant negative direct effects on both the plant growth indicators and total alkaloid content of S. alopecuroides (p < 0.01). This study provides new insights into the interactions among rhizosphere soil environment, rhizosphere microbiota, plant growth, and alkaloid accumulation under water and nitrogen regulation, offering a scientific basis for the water and nitrogen management in the cultivation of S. alopecuroides.

Noviherbaspirillum album sp. nov., an airborne bacteria isolated from an urban area of Beijing, China

A Gram-negative, ellipsoidal to short-rod-shaped, motile bacterium was isolated from Beijing's urban air. The isolate exhibited the closest kinship with Noviherbaspirillum aerium 122213-3T, exhibiting 98.4 % 16S rRNA gene sequence similarity. Phylogenetic analyses based on 16S rRNA gene sequences and genomes showed that it clustered closely with N. aerium 122213-3T, thus forming a distinct phylogenetic lineage within the genus Noviherbaspirillum. The average nucleotide identity and digital DNA-DNA hybridization values between strain I16B-00201T and N. aerium 122213-3T were 84.6 and 29.4 %, respectively. The respiratory ubiquinone was ubiquinone 8. The major fatty acids (>10 %) were summed feature 3 (C16:1ω6c/C16:1ω7c, 43.3 %), summed feature 8 (C18:1ω7c/C18:1ω6c, 15.9 %) and C12:0 (11.0 %). The polyamine profile showed putrescine as the predominant compound. The polar lipid profile consisted of diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, phosphatidylcholine, unknown lipids and unknown phosphatidylaminolipids. The phenotypic, phylogenetic and chemotaxonomic results consistently supported that strain I16B-00201T represented a novel species of the genus Noviherbaspirillum, for which the name Noviherbaspirillum album sp. nov. is proposed, with I16B-00201T (=CPCC 100848T=KCTC 52095T) designated as the type strain. Its DNA G+C content is 59.4 mol%. Pan-genome analysis indicated that some Noviherbaspirillum species possess diverse nitrogen and aromatic compound metabolism pathways, suggesting their potential value in pollutant treatment.

Noviherbaspirillum aridicola sp. nov., isolated from an arid soil in Pakistan

Strain NCCP-691T was isolated from a soil sample collected from an arid soil in Karak, Khyber Pakhtunkhwa, Pakistan. Phenotypically, the cells were Gram-stain-negative, aerobic and motile rods. The organism was able to grow between 20-40 °C (optimum at 30-37 °C), at pH 5.5-8.0 (optimum at pH 7.0-7.2) and tolerated 0-1.5% NaCl (w/v) (optimum at 0-0.5). Based on 16S rRNA gene sequences, strain NCCP-691T formed a distinct phylogenetic clade with Noviherbaspirillum arenae, N. agri, N. denitrificans and N. autotrophicum (having sequence similarities of 99.0; 98.1; 98.0 and 97.7% respectively). Phylogenetic analyses based on the whole genome sequences confirmed that strain NCCP-691T should be affiliated to the genus Noviherbaspirillum. The average nucleotide identity values compared to other species of Noviherbaspirillum were below 95-96 % and digital DNA-DNA hybridization values were less than 70 %. Chemotaxonomic analyses showed that the strain had ubiquinone-8, as the only respiratory quinine. The major cellular fatty acids were summed feature 3 (C16 : 1 ω 7 c/C16 : 1 ω 6 c, 35.9 %), summed feature 8 (C18 : 1 ω 7 c/C18 : 1 ω 6 c, 26.9 %) and C16 : 0 (22.9 %) and the polar lipid profile was composed of diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine and phosphatidylcholine. The genomic DNA G+C content was 65.5 mol% (from draft genome). Genome analyses showed that strain NCCP-691T had terpene and arylpolyene biosynthetic genes clusters and genes related to resistance against heavy metals. Based on phylogenetic analyses, phenotypic features and genomic comparison, it is proposed that strain NCCP-691T is a novel species of the genus Noviherbaspirillum and the name Noviherbaspirillum aridicola sp. nov. is proposed. Type strain is NCCP-691T (=KCTC 52721T=CGMCC 1.13600T).

Noviherbaspirillum pedocola sp. nov., isolated from oil-contaminated experimental soil

An orange-coloured, rod-shaped, and aerobic bacterial strain DKR-6 ^T was isolated from oil-contaminated experimental soil. The strain was Gram-stain-negative, catalase and oxidase positive, and grew at temperature 10-42 °C, at pH 5.5-9.5, and at 0-3.0% (w/v) NaCl concentration. The phylogenetic analysis and 16S rRNA gene sequence analysis suggested that the strain DKR-6 ^T was affiliated to the genus Noviherbaspirillum, with the closest species being Noviherbaspirillum massiliense JC206^T (96.3% sequence similarity). The chemotaxonomic profiles revealed the presence of phosphatidylethanolamine, phosphatidylglycerol, diphosphatidylglycerol, and phosphatidylcholine as the principal polar lipids; C_16:0, C_17:0 cyclo, summed feature 3 (C_16:1ω7c and/or C_{16: 1}ω6c), and summed feature 8 (C_18:1ω7c/or C_18:1ω6c) as the main fatty acids; and Q-8 as a sole ubiquinone. The DNA G + C content was 61.6%. The polyphasic taxonomic features illustrated in this study clearly implied that strain DKR-6 ^T represents a novel species in the genus Noviherbaspirillum, for which the name Noviherbaspirillum pedocola sp. nov. is proposed with the type strain DKR-6 ^T (= KACC 22074 ^T = NBRC 114727 ^T).

Noviherbaspirillum aerium sp. nov., isolated from air

A Gram-stain-negative, strictly aerobic, non-spore-forming, rod-shaped, motile with polar flagella and pale-orange bacterium, designated strain 122213-3^T, was isolated from air, collected at the foot of the Xiangshan Mountain, located in Beijing, PR China. Optimal growth occurred at 28 °C, at pH 7 and in the presence of 0-1 % (w/v) NaCl. Phylogenetic analyses based on 16S rRNA gene sequences revealed that 122213-3^T clustered with species of the genus Noviherbaspirillum and formed a distinct sublineage, showing highest similarities to Noviherbaspirillum malthae CC-AFH3^T (96.88 %), Noviherbaspirillum massiliense JC206^T (95.78 %) and Noviherbaspirillum aurantiacum SUEMI08^T (95.78 %). The predominant cellular fatty acids were summed feature 3 (C_16 : 1  ω6c and/or C_16 : 1  ω7c), summed feature 8 (C_18 : 1  ω7c and/or C_18 : 1  ω6c) and C_16 : 0. The predominant quinone was ubiquinone 8 (Q-8). The polar lipids comprised phosphatidylethanolamine, phosphatidylglycerol, unidentified phospholipid and two unidentified polar lipids. The polyamine pattern showed the presence of putrescine as the major polyamine, with minor amounts of 2-hydroxyputrescine. The DNA G+C content was 60.1 mol%. The phylogenetic analysis and physiological and biochemical data showed that strain 122213-3^T should be classified as representing a novel species in the genus Noviherbaspirillum, for which the name Noviherbaspirillum aerium sp. nov. is proposed. The type strain of N. aerium is 122213-3^T (=CFCC 14286^T=LMG 30131^T).

Noviherbaspirillum galbum sp. nov., a bacterium isolated from soil

A Gram-stain-negative, aerobic, non-motile and yellow-colored bacterium, strain 17J57-3 ^T, was isolated from soil collected in Pyeongchang city, Korea. Phylogenetic analyses based on 16S rRNA gene sequences revealed that strain 17J57-3 ^T formed a distinct lineage within the family Oxalobacteraceae (order Burkholderiales, class Betaproteobacteria). Strain 17J57-3 ^T was the most closely related to Noviherbaspirillum humi U15^T (96.4% 16S rRNA gene sequence similarity) and Noviherbaspirillum massiliense JC206^T (96.2%). The draft genome size of strain 17J57-3 ^T was 6,117,206 bp. Optimal growth occurred at 30 °C, pH 7.0 without NaCl. The predominant cellular fatty acids were summed feature 3 (C_16:1 ω6c/C_16:1 ω7c) and C_16:0. The major respiratory quinone was Q-8. The major polar lipids were diphosphatidylglycerol, phosphatidylglycerol and phosphatidylethanolamine. Biochemical, chemotaxonomic and phylogenetic analyses indicated that strain 17J57-3 ^T represents a novel bacterial species within the genus Noviherbaspirillum, for which the name Noviherbaspirillum galbum is proposed. The type strain of Noviherbaspirillum galbum is 17J57-3 ^T (= KCTC 62213 ^T = NBRC 114384 ^T).

Quisquiliibacterium transsilvanicum gen. nov., sp. nov., a novel betaproteobacterium isolated from a waste-treating bioreactor

A new betaproteobacterium, CGI-09^T, was isolated from an activated sludge bioreactor which treated landfill leachate. Based on 16S rRNA gene sequence analysis, the new strain shared the highest pairwise similarity values with members of the order Burkholderiales: Derxia gummosa IAM 13946^T (family Alcaligenaceae), 93.7 % and Lautropia mirabilis DSM 11362^T (family Burkholderiaceae), 93.6 %. Cells of strain CGI-09^T were rod-shaped and non-motile. The new strain was oxidase and catalase positive and capable of reducing nitrate to nitrite. The predominant fatty acids were C16 : 1 ω7c, C16 : 0, cycloC17 : 0 and C18 : 1 ω7c, the major respiratory quinone was Q-8, and the detected polar lipids were phosphatidylglycerol, diphosphatidylglycerol, phosphatidylethanolamine and an unknown phospholipid. The G+C content of the genomic DNA of strain CGI-09^T was 70.2 mol%. The new bacterium can be distinguished from the members of genera Derxia and Lautropia based on its non-motile cells, arginine dihydrolase activity, its high cyclo C17 : 0 fatty acid content and the lack of hydroxy fatty acids. On the basis of the phenotypic, chemotaxonomic and molecular data, strain CGI-09^T is considered to represent a new genus and species within the family Burkholderiaceae, for which the name Quisquiliibacterium transsilvanicum gen. nov., sp. nov. is proposed. The type strain is CGI-09^T (=DSM 29781^T=JCM 31785^T).