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Paenibacillus sinensis sp. nov., a nitrogen-fixing species isolated from plant rhizospheres

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Abstract

Two strains HN-1T and 39 were isolated from rhizospheres of different plants grown in different regions of PR China. The two strains exhibited high nitrogenase activities and possessed almost identical 16S rRNA gene sequences. The average nucleotide identity (ANI) and digital DNA–DNA hybridization (dDDH) values between the two strains were 99.9 and 99.8%, respectively, suggesting that they belong to one species. Phylogenetic analysis based on the 16S rRNA gene sequence showed that strains HN-1T and 39 are the members of the genus Paenibacillus and both strains exhibited 99.5% similarity to Paenibacillus stellifer DSM 14472T and the both strains represented a separate lineage from all other Paenibacillus species. However, the ANI of type strain HN-1T with P. stellifer DSM 14472T was 90.69, which was below the recommended threshold value (< 95–96% ANI). The dDDH showed 42.1% relatedness between strain HN-1T and P. stellifer DSM 14472T, which was lower than the recommended threshold value (dDDH < 70%). The strain HN-1T contain anteiso-C15:0 as major fatty acids and MK-7 as predominant isoprenoid quinone. The major polar lipids were diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, four aminophospholipids and an unidentified glycolipid. Unlike the most closely related P. stellifer DSM 14472T, strain HN-1T or 39 was positive for catalase reaction. Distinct phenotypic and genomic characterisations from previously described taxa support the classification of strains HN-1T or 39 as representatives of a novel species of the genus Paenibacillus, for which the name Paenibacillus sinensis is proposed, with type strains HN-1T (=CGMCC 1.18902, JCM 34,620), and reference strain 39 (=CGMCC 1.18879, JCM 34,616), respectively.

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The GenBank accession numbers for 16S rRNA gene sequences of strains HN-1T and 39 are MF967304 and MZ153121, respectively. The draft genome sequences of strains HN-1T and 39 have been deposited at NCBI under the accession no. JAHCMB000000000 and JAHBAZ000000000.

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Funding

This work was supported by the National Key Research and Development Program of China (No. 2019YFA0904700) and the National Natural Science Foundation of China (No. 32000048).

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  1. State Key Laboratory for Agrobiotechnology, China Agricultural University, Beijing, 100193, People’s Republic of China

    Qin Li, Yashi Li, Xiaomeng Liu & Sanfeng Chen

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10482_2021_1677_MOESM1_ESM.tif

Fig. S1 Maximum-likelihood phylogenetic tree based on gyrB gene sequences showing the position of strains HN-1T and 39 among species of the genus Paenibacillus. Bootstrap analyses were performed with 1000 cycles. Only bootstrap values >50 % are shown at the branch points. Bar 0.01 substitutions per nucleotide positions (TIF 13883 KB)

Fig. S2 Organization of nif, anf and nif-like genes in type strain HN-1T and P. stellifer DSM 14472T (TIF 15905 KB)

10482_2021_1677_MOESM3_ESM.tif

Fig. S3 Colony and strain morphology, (a) Colony morphology of strain HN-1T and light micrograph of endospores which stained with specific endospores staining method. Endospores-staining was performed by the modified schaeffer-fulton method according to Mormak et al. (1985) (TIF 13947 KB)

10482_2021_1677_MOESM4_ESM.tif

Fig. S4 Two-dimensional TLC plate of polar lipids extracted from strains HN-1T (a) and 39 (b). The plate was sprayed with 10% (v/v) molybdophosphoric aicd to show all polar lipids present. PE, phosphatidylethanolamine; PG, phosphatidylglycerol; DPG, diphosphatidylglycerol; PL, unidentified phosphoglycolipid; APL, aminophospholipid; GL, unidentified glycolipid (TIF 12719 KB)

10482_2021_1677_MOESM5_ESM.docx

Table S1 Fatty acid content (%) of strain HN-1T and 39 and some other type strains of the Paenibacillus genus (DOCX 15 KB)

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Li, Q., Li, Y., Liu, X. et al. Paenibacillus sinensis sp. nov., a nitrogen-fixing species isolated from plant rhizospheres. Antonie van Leeuwenhoek 115, 7–18 (2022). https://doi.org/10.1007/s10482-021-01677-6

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