Mapping the molecular landscape of Lotus japonicus nodule organogenesis through spatiotemporal transcriptomics.

Legumes acquire nitrogen-fixing ability by forming root nodules. Transferring this capability to more crops could reduce our reliance on nitrogen fertilizers, thereby decreasing environmental pollution and agricultural production costs. Nodule organogenesis is complex, and a comprehensive transcriptomic atlas is crucial for understanding the underlying molecular events. Here, we utilized spatial transcriptomics to investigate the development of nodules in the model legume, Lotus japonicus. Our investigation has identified the developmental trajectories of two critical regions within the nodule: the infection zone and peripheral tissues. We reveal the underlying biological processes and provide gene sets to achieve symbiosis and material exchange, two essential aspects of nodulation. Among the candidate regulatory genes, we illustrate that LjNLP3, a transcription factor belonging to the NIN-LIKE PROTEIN family, orchestrates the transition of nodules from the differentiation to maturation. In summary, our research advances our understanding of nodule organogenesis and provides valuable data for developing symbiotic nitrogen-fixing crops.

Streptomyces albipurpureus sp. nov., a novel actinobacterium with antimicrobial activity isolated from the rhizospheric soil of Fritillaria cirrhosa D. Don.

A novel actinobacterium, designated strain CWNU-1T, was isolated from the rhizospheric soil of Fritillaria cirrhosa D. Don and examined using a polyphasic taxonomic approach. The organism developed pale blue aerial mycelia that was simply branched and terminated in open or closed coils of three or more volutions on International Streptomyces Project 3 agar. Spores were ellipsoidal to cylindrical with wrinkled surfaces. The strain showed high 16S rRNA gene sequence similarity to Streptomyces kurssanovii NBRC 13192T (98.8 %), Streptomyces xantholiticus NBRC 13354T (98.7 %) and Streptomyces peucetius JCM 9920T (98.6 %). The phylogenetic result based on 16S rRNA gene and genome sequences clearly demonstrated that strain CWNU-1T formed an independent phylogenetic lineage. On the basis of orthologous average nucleotide identity, CWNU-1T was most closely related to Streptomyces inusitatus NBRC 13601T with 79.3 % identity. The results of the digital DNA-DNA hybridization analysis also indicated low levels of relatedness with other species, as the highest value was observed with S. inusitatus NBRC 13601T (25.3 %). With reference to phenotypic characteristics, phylogenetic data, orthologous average nucleotide identity and digital DNA-DNA hybridization results, strain CWNU-1T was readily distinguished from its most closely related strains and classified as representing a novel species, for which the name Streptomyces albipurpureus sp. nov. is proposed. The type strain is CWNU-1T (=CGMCC 4.7758T=MCCC 1K07402T=JCM 35391T).

Micromonospora parathelypteridis sp. nov., an endophytic actinomycete with antifungal activity isolated from the root of Parathelypteris beddomei (Bak.) Ching.

A novel endophytic actinomycete with antifungal activity, designated strain NEAU-JXY5T, was isolated from the root of Parathelypteris beddomei (Bak.) Ching. Strain NEAU-JXY5T showed closest 16S rRNA gene sequence similarity to Micromonospora luteifusca GUI2T (99.31 %), and phylogenetically clustered with Micromonospora noduli GUI43T (99.24 %), 'Micromonospora lycii' NEAU-gq11 (99.19 %), 'Micromonospora zeae' NEAU-gq9 (99.12 %), Micromonospora saelicesensis Lupac 09T (98.97 %), Micromonospora vinacea GUI63T (98.96 %), 'Micromonospora jinlongensis' NEAU-GRX11 (98.91 %), Micromonospora profundi DS3010T (98.77 %), Micromonospora zamorensis CR38T (98.76 %), Micromonospora chokoriensis 2-19(6)T (98.71 %), Micromonospora lupini Lupac 14NT (98.69 %), Micromonospora ureilytica GUI23T (98.69 %), Micromonospora violae NEAU-zh8T (98.57 %) and Micromonospora taraxaci NEAU-P5T (98.37 %). Phylogenetic analysis based on gyrB gene sequences also indicated that the isolate clustered with the above strains except M. violae NEAU-zh8T. A combination of DNA-DNA hybridization results and some phenotypic characteristics indicated that the strain could be readily distinguished from these closest phylogenetic relatives. Therefore, it is concluded that strain NEAU-JXY5T represents a novel species of the genus Micromonospora, for which the name Micromonospora parathelypteridis sp. nov. is proposed. The type strain is NEAU-JXY5T (=CGMCC 4.7347T=DSM 103125T).

Verrucosispora sonchi sp. nov., a novel endophytic actinobacterium isolated from the leaves of common sowthistle (Sonchus oleraceus L.).

A novel actinobacterium, designated strain NEAU-QY3T, was isolated from the leaves of Sonchus oleraceus L. and examined using a polyphasic taxonomic approach. The organism formed single spores with smooth surface on substrate mycelia. Phylogenetic analysis based on the 16S rRNA gene sequence indicated that the strain had a close association with the genus Verrucosispora and shared the highest sequence similarity with Verrucosispora qiuiae RtIII47T (99.17 %), an association that was supported by a bootstrap value of 94 % in the neighbour-joining tree and also recovered with the maximum-likelihood algorithm. The strain also showed high 16S rRNA gene sequence similarities to Xiangella phaseoli NEAU-J5T (98.78 %), Jishengella endophytica 202201T (98.51 %), Micromonospora eburnea LK2-10T (98.28 %), Verrucosispora lutea YIM 013T (98.23 %) and Salinispora pacifica CNR-114T (98.23 %). Furthermore, phylogenetic analysis based on the gyrB gene sequences supported the conclusion that strain NEAU-QY3T should be assigned to the genus Verrucosispora. However, the DNA-DNA hybridization relatedness values between strain NEAU-QY3T and V. qiuiae RtIII47T and V. lutea YIM 013T were below 70 %. With reference to phenotypic characteristics, phylogenetic data and DNA-DNA hybridization results, strain NEAU-QY3T was readily distinguished from its most closely related strains and classified as a new species, for which the name Verrucosispora sonchi sp. nov. is proposed. The type strain is NEAU-QY3T (=CGMCC 4.7312T=DSM 101530T).

Streptomyces camponoticapitis sp. nov., an actinomycete isolated from the head of an ant (Camponotus japonicus Mayr).

A novel single-spore-producing actinomycete, designated strain 2H-TWYE14T, was isolated from the head of an ant (Camponotus japonicus Mayr) and characterized using a polyphasic approach. 16S rRNA gene sequence analysis showed that strain 2H-TWYE14T belongs to the genus Streptomyces, with highest sequence similarity to Streptomyces niveus NRRL 2466T (98.84 %). Analysis based on the gyrB gene also indicated that strain 2H-TWYE14T should be assigned to the genus Streptomyces. The chemotaxonomic properties of strain 2H-TWYE14T were consistent with those of members of the genus Streptomyces. The cell wall contained ll-diaminopimelic acid. The predominant menaquinones were MK-9(H6), MK-9(H8) and MK-9(H4). The phospholipid profile consisted of diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylinositol and phosphatidylinositol mannoside. The major fatty acids were iso-C16 : 0 and iso-C15 : 0. DNA-DNA hybridization experiments and phenotypic tests were carried out between strain 2H-TWYE14T and its phylogenetically closely related strain S. niveus JCM 4251T, which further clarified their relatedness and demonstrated that 2H-TWYE14T could be distinguished from S. niveus. Therefore, it is concluded that strain 2H-TWYE14T can be classified as representing a novel species of the genus Streptomyces, for which the name Streptomyces camponoticapitis sp. nov. is proposed. The type strain is 2H-TWYE14T (=DSM 100523T=CGMCC 4.7275T).

Streptomyces bryophytorum sp. nov., an endophytic actinomycete isolated from moss (Bryophyta).

A novel endophytic actinomycete, designated strain NEAU-HZ10(T) was isolated from moss and characterised using a polyphasic approach. The strain was found to have morphological and chemotaxonomic characteristics typical of the genus Streptomyces. Strain NEAU-HZ10(T) formed grayish aerial mycelia, which differentiated into straight to flexuous chains of cylindrical spores. The cell wall peptidoglycan was found to contain LL-diaminopimelic acid. Predominant menaquinones were identified as MK-9(H6) and MK-9(H8). The polar lipid profile was found to consist of phosphatidylethanolamine, phosphatidylinositol and two unidentified phospholipids. The major fatty acids were identified as iso-C16:0, anteiso-C15:0 and C16:0. 16S rRNA gene sequence similarity studies showed that strain NEAU-HZ10(T) belongs to the genus Streptomyces and exhibits high sequence similarity to Streptomyces cocklensis DSM 42063(T) (98.9 %). Phylogenetic analysis based on the 16S rRNA gene sequence indicated that strain NEAU-HZ10(T) clustered with S. cocklensis DSM 42063(T), Streptomyces yeochonensis CGMCC 4.1882(T) (98.7 %), Streptomyces paucisporeus CGMCC 4.2025(T) (98.4 %) and Streptomyces yanglinensis CGMCC 4.2023(T) (98.1 %). However, a combination of DNA-DNA hybridisation results and some phenotypic characteristics indicated that strain NEAU-HZ10(T) can be distinguished from its phylogenetically closely related strains. Therefore, it is proposed that strain NEAU-HZ10(T) represents a novel species of the genus Streptomyces for which the name Streptomyces bryophytorum sp. nov. is proposed. The type strain is NEAU-HZ10(T) (= CGMCC 4.7151(T) = DSM 42138(T)).

Dactylosporangium solaniradicis sp. nov., a novel actinobacterium isolated from a root of tomato (Solanum lycopersicum L.).

A novel actinobacterium, designated strain NEAU-FJL2(T), was isolated from a tomato root (Solanum lycopersicum L.) and characterised using a polyphasic approach. Morphological and chemotaxonomic properties of strain NEAU-FJL2(T) are consistent with the description of the genus Dactylosporangium. Finger-shaped sporangia were observed to form on short sporangiophores branching from the substrate hyphae. The cell wall peptidoglycan was found to contain meso- and 3-hydroxy-diaminopimelic acids; arabinose, mannose, rhamnose and xylose were found as whole-cell sugars. The phospholipid profile was found to consist of diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol and phosphatidylinositol. The predominant menaquinones were identified as MK-9(H8) and MK-9(H6). The major fatty acids were identified as iso-C16:0, C16:1 ω7c and iso-C15:0. Phylogenetic analysis based on 16S rRNA gene sequences demonstrated that strain NEAU-FJL2(T) belongs to the genus Dactylosporangium, with Dactylosporangium sucinum JCM 19831(T) (99.3 % 16S rRNA gene sequence similarity), Dactylosporangium darangshiense JCM 17441(T) (99.2 %), Dactylosporangium fulvum JCM 5631(T) (98.9 %) and Dactylosporangium roseum JCM 3364(T) (98.8 %) as the nearest phylogenetic relatives. However, a combination of DNA-DNA hybridization results and some phenotypic characteristics demonstrated that strain NEAU-FJL2(T) can be distinguished from them. Consequently, it is proposed that strain NEAU-FJL2(T) represents a novel species of the genus Dactylosporangium, for which the name Dactylosporangium solaniradicis sp. nov. is proposed. The type strain is NEAU-FJL2(T) (=CGMCC 4.7302(T) = DSM 100814(T)).

Plantactinospora sonchi sp. nov., an actinobacterium isolated from the leaves of common sowthistle (Sonchus oleraceus L.).

A novel actinobacterium, designated strain NEAU-QY2T, was isolated from the leaves of Sonchus oleraceus L. specimen, collected from Wuchang, Heilongjiang Province, China. A polyphasic study was carried out to establish the taxonomic position of this strain. The organism formed single spores with rough surfaces on substrate mycelia. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain NEAU-QY2T belonged to the genus Plantactinospora and formed a monophyletic clade with its closest related strains Plantactinospora endophytica YIM 68255T (99.2 % 16S rRNA gene sequence similarity), Plantactinospora veratri NEAU-FHS4T (98.8 %) and Plantactinospora mayteni YIM 61359T(98.7 %), an association that was supported by a bootstrap value of 90 % in the neighbor-joining tree and also recovered with the maximum-likelihood algorithm. However, DNA-DNA hybridization values between strain NEAU-QY2T and the three closely related strains were below 70 %. With reference to phenotypic characteristics, phylogenetic data and DNA-DNA hybridization results, strain NEAU-QY2T was distinguished from closely related strains and is classified as representing a novel species of the genus Plantactinospora, for which the name Plantactinospora sonchi sp. nov. is proposed. The type strain is NEAU-QY2T (=CGMCC4.7216T=JCM 30345T).

Actinoplanes rhizophilus sp. nov., an actinomycete isolated from the rhizosphere of Sansevieria trifasciata Prain.

A novel actinomycete, designated strain NEAU-A-2T, was isolated from the rhizosphere soil of Sansevieria trifasciata Prain collected from Heilongjiang province, north-east China. The taxonomic status of this organism was established using a polyphasic approach. The isolate formed irregular sporangia containing motile spores on the substrate mycelium. The whole-cell sugars were xylose and galactose. The predominant menaquinones were MK-9(H10), MK-9(H2), MK-10(H2) and MK-10(H4). The major fatty acids were iso-C15 : 0, iso-C16 : 0 and anteiso-C15 : 0. The polar lipids were diphosphatidylglycerol, phosphatidylmonomethylethanolamine, phosphatidylethanolamine, phosphatidylinositol, three unidentified phospholipids and an unidentified glycolipid. 16S rRNA gene sequence similarity studies showed that strain NEAU-A-2T belongs to the genus Actinoplanes with the highest sequence similarities to Actinoplanes globisporus NBRC 13912T (97.7 % 16S rRNA gene sequence similarity), Actinoplanes ferrugineus IMSNU 22125T (97.5 %), Actinoplanes toevensis MN07-A0368T (97.2 %) and Actinoplanes rishiriensis NBRC 108556T (97.2 %); similarities to type strains of other species of this genus were < 97 %. Two tree-making algorithms showed that strain NEAU-A-2T formed a distinct clade with A. globisporus NBRC 13912T and A. rishiriensis NBRC 108556T. However, low DNA-DNA relatedness values allowed the isolate to be differentiated from the above-mentioned two species of the genus Actinoplanes. Moreover, strain NEAU-A-2T could also be distinguished from the most closely related species by morphological and physiological characteristics. Therefore, in conclusion, isolate NEAU-A-2T represents a novel species of the genus Actinoplanes, for which the name Actinoplanes rhizophilus sp. nov. is proposed. The type strain is NEAU-A-2T ( = CGMCC 4.7133T = DSM 46672T).

Sphaerisporangium corydalis sp. nov., isolated from the root of Corydalis yanhusuo L.

Two Gram-stain positive, aerobic actinomycete strains, designated NEAU-YHS12 and NEAU-YHS15(T), were isolated from the root of Corydalis yanhusuo L. collected from Wuchang, Heilongjiang Province, northeast China. Phylogenetic analysis of 16S rRNA gene sequences showed that the two strains are closely related to one another (99.8 % similarity), and had the closest relationship with Sphaerisporangium cinnabarinum JCM 3291(T) (98.7, 98.6 %), Sphaerisporangium flaviroseum YIM 48771(T) (98.6, 98.6 %), Sphaerisporangium melleum JCM 13064(T) (98.5, 98.4 %) and Sphaerisporangium dianthi NEAU-CY18(T) (98.4, 98.4 %). DNA-DNA hybridization value between strains NEAU-YHS12 and NEAU-YHS15(T) was 82 ± 1.4 %, and the values between the two strains and the closely related type strains were well below 70 %. The two strains also shared a number of phenotypic characteristics that were distinct from the closely related species. Both strains were observed to contain MK-9(H6), MK-9(H4) and MK-9(H2) as the detected menaquinones. The cell wall peptidoglycan was found to contain meso-diaminopimelic acid. The phospholipid profiles were found to contain diphosphatidylglycerol, phosphatidylmethylethanolamine, phosphatidylethanolamine, phosphatidylinositol, phosphatidylinositol mannoside, phosphoglycolipid, and an unidentified phospholipid. The major fatty acids were identified as iso-C16:0, C17:1 ω7c, C18:0 and iso-C15:0. On the basis of the genetic and phenotypic properties, it is proposed that strains NEAU-YHS15(T) and NEAU-YHS12 be classified as representatives of a novel species of the genus Sphaerisporangium, for which the name Sphaerisporangium corydalis sp. nov is proposed. The type strain is NEAU-YHS15(T) (CGMCC 4.7148(T) = DSM46732(T)).

Streptosporangium sonchi sp. nov. and Streptosporangium kronopolitis sp. nov., two novel actinobacteria isolated from a root of common sowthistle (Sonchus oleraceus L.) and a millipede (Kronopolites svenhedind Verhoeff).

Two novel actinobacteria, designated strains NEAU-QS7(T) and NEAU-ML10(T), were isolated from a root of Sonchus oleraceus L. and a Kronopolites svenhedind Verhoeff specimen, respectively, collected from Wuchang, Heilongjiang Province, China. A polyphasic study was carried out to establish the taxonomic positions of these strains. The two strains were observed to form abundant aerial hyphae that differentiated into spherical spore vesicles. The phylogenetic analysis based on the 16S rRNA gene sequences of strains NEAU-QS7(T) and NEAU-ML10(T) showed that the two novel isolates exhibited 99.7 % 16S rRNA gene sequence similarity with each other and that they are most closely related to Streptosporangium shengliense NEAU-GH7(T) (99.1, 99.0 %) and Streptosporangium longisporum DSM 43180(T) (99.1, 99.0 %). However, the DNA-DNA hybridization value between strains NEAU-QS7(T) and NEAU-ML10(T) was 46.5 %, and the values between the two strains and their closest phylogenetic relatives were also below 70 %. With reference to phenotypic characteristics, phylogenetic data and DNA-DNA hybridization results, the two strains can be distinguished from each other and their closest phylogenetic relatives. Thus, strains NEAU-QS7(T) and NEAU-ML10(T) represent two novel species of the genus Streptosporangium, for which the names Streptosporangium sonchi sp. nov. and Streptosporangium kronopolitis sp. nov. are proposed. The type strains are NEAU-QS7(T) (=CGMCC 4.7142(T) =DSM 46717(T)) and NEAU-ML10(T) (=CGMCC 4.7153(T) =DSM 46720(T)), respectively.

Actinomycetospora rhizophila sp. nov., an actinomycete isolated from rhizosphere soil of a peace lily (Spathi phyllum Kochii).

A novel actinomycete, designated strain NEAU-B-8(T), was isolated from the rhizosphere soil of a peace lily (Spathi phyllum Kochii) collected from Heilongjiang province, north-east China. Key morphological and physiological characteristics as well as chemotaxonomic features of strain NEAU-B-8(T) were congruent with the description of the genus Actinomycetospora , such as the major fatty acids, the whole-cell hydrolysates, the predominant menaquinone and the phospholipid profile. The 16S rRNA gene sequence analysis revealed that strain NEAU-B-8(T) shared the highest sequence similarities with Actinomycetospora lutea JCM 17982(T) (99.3% 16S rRNA gene sequence similarity), Actinomycetospora chlora TT07I-57(T) (98.4 %), Actinomycetospora straminea IY07-55(T) (98.3%) and Actinomycetospora chibensis TT04-21(T) (98.2%); similarities to type strains of other species of this genus were lower than 98%. The phylogenetic tree based on 16S rRNA gene sequences showed that strain NEAU-B-8(T) formed a distinct branch with A. lutea JCM 17982(T) that was supported by a high bootstrap value of 97% in the neighbour-joining tree and was also recovered with the maximum-likelihood algorithm. However, the DNA-DNA relatedness between strain NEAU-B-8(T) and A. lutea JCM 17982(T) was found to be 50.6 ± 1.2%. Meanwhile, strain NEAU-B-8(T) differs from other most closely related strains in phenotypic properties, such as maximum NaCl tolerance, hydrolysis of aesculin and decomposition of urea. On the basis of the morphological, physiological, chemotaxonomic, phylogenetic and DNA-DNA hybridization data, we conclude that strain NEAU-B-8(T) represents a novel species of the genus Actinomycetospora , named Actinomycetospora rhizophila sp. nov. The type strain is NEAU-B-8(T). ( = CGMCC 4.7134(T) =DSM 46673(T)).