Complete Genome Sequence Data of Bacillus altitudinis LZP02, a Bacterium from the Rice Rhizosphere, for Studying the Promotion of Plant Growth

HomeMolecular Plant-Microbe Interactions®Vol. 35, No. 5Complete Genome Sequence Data of Bacillus altitudinis LZP02, a Bacterium from the Rice Rhizosphere, for Studying the Promotion of Plant Growth PreviousNext RESOURCE ANNOUNCEMENT OPENOpen Access licenseComplete Genome Sequence Data of Bacillus altitudinis LZP02, a Bacterium from the Rice Rhizosphere, for Studying the Promotion of Plant GrowthHuiwen Jiao, Weihui Xu, Wenjing Chen, Yunlong Hu, Renmao Tian, and Zhigang WangHuiwen JiaoSchool of Life Science and Agriculture Forestry, Qiqihar University, Qiqihar, Heilongjiang 161006, ChinaHeilongjiang Provincial Technology Innovation Center of Agromicrobial Preparation Industrialization, Qiqihar 161006, China, Weihui XuSchool of Life Science and Agriculture Forestry, Qiqihar University, Qiqihar, Heilongjiang 161006, ChinaHeilongjiang Provincial Technology Innovation Center of Agromicrobial Preparation Industrialization, Qiqihar 161006, China, Wenjing ChenSchool of Life Science and Agriculture Forestry, Qiqihar University, Qiqihar, Heilongjiang 161006, ChinaHeilongjiang Provincial Technology Innovation Center of Agromicrobial Preparation Industrialization, Qiqihar 161006, China, Yunlong HuSchool of Life Science and Agriculture Forestry, Qiqihar University, Qiqihar, Heilongjiang 161006, ChinaHeilongjiang Provincial Technology Innovation Center of Agromicrobial Preparation Industrialization, Qiqihar 161006, China, Renmao TianInstitute for Food Safety and Health, Illinois Institute of Technology, Chicago, IL 60501, U.S.A., and Zhigang Wang†Corresponding author: Z. Wang; E-mail Address: wangzhigang@qqhru.edu.cnhttps://orcid.org/0000-0002-0981-6597School of Life Science and Agriculture Forestry, Qiqihar University, Qiqihar, Heilongjiang 161006, ChinaHeilongjiang Provincial Technology Innovation Center of Agromicrobial Preparation Industrialization, Qiqihar 161006, China AffiliationsAuthors and Affiliations Huiwen Jiao1 2 Weihui Xu1 2 Wenjing Chen1 2 Yunlong Hu1 2 Renmao Tian3 Zhigang Wang1 2 † 1School of Life Science and Agriculture Forestry, Qiqihar University, Qiqihar, Heilongjiang 161006, China 2Heilongjiang Provincial Technology Innovation Center of Agromicrobial Preparation Industrialization, Qiqihar 161006, China 3Institute for Food Safety and Health, Illinois Institute of Technology, Chicago, IL 60501, U.S.A. Published Online:13 Apr 2022https://doi.org/10.1094/MPMI-01-22-0012-AAboutSectionsView articlePDFSupplemental ToolsAdd to favoritesDownload CitationsTrack Citations ShareShare onFacebookTwitterLinked InRedditEmailWechat View articleGenome AnnouncementPlant-growth-promoting rhizobacteria (PGPR) refer to a class of bacteria that colonize plant roots and have beneficial effects on plant development (Akinrinlola et al. 2018). Biocontrol fertilizers made from PGPR are increasingly applied in sustainable agriculture. In a previous study, Bacillus altitudinis LZP02 (formerly B. pumilus LZP02) was found to produce auxin and siderophores (Liu et al. 2018). In addition, B. altitudinis LZP02 promoted the absorption of P, Ca, and Mg ions through the colonization of rice roots, enhanced enzyme activities, and chlorophyll contents in rice (Liu et al. 2020). B. altitudinis LZP02 has been deposited in the China Center for Type Culture Collection (number M 2018598). The hemolytic test showed that the strain is not pathogenic. However, in-depth research on the promotion mechanism of PGPRs in the rice rhizosphere has not been carried out to date, even though the elucidation of such mechanisms is extremely important and urgently needed. In this study, we determined the complete genome sequence of B. altitudinis LZP02 as a valuable resource for the clarification of the growth-promoting ability of this strain on rice roots.Strain LZP02 was identified as B. pumilus at the species level primarily. After completing the whole-genome sequencing, it was reclassified as B. altitudinis, based on the analysis of 16S ribosomal RNA (rRNA) gene and housekeeping genes. The genomic DNA of LZP02 was extracted using a Qiagen genomic tip (Qiagen) following the manufacturer's protocol. The harvested DNA was detected by agarose gel electrophoresis and quantified by Qubit assays (Invitrogen). A library was prepared using the high-quality genomic DNA of LZP02 using a ligation sequencing kit (Oxford Nanopore Technology). The library was sequenced using a single PromethION flowcell (FLO-PRO002; Oxford Nanopore Technology) for 72 h in Biomarker Technologies Co., Ltd.The sequencing yielded 234,696 clean reads with a total size of 2,237,493,616 bp and N50 length of 14,915 bp, which corresponds to 589.7× sequence depth. The reads after the quality control were assembled by Canu v1.5. Finally, we polished the assemblies using Pilon v1.22. In general, polishing significantly improved the total lengths of Oxford Nanopore Technology assemblies, and increased N50 length to 3,763,082 bp. Automatic annotation was performed as well, using the Prokaryotic Genome Annotation Pipeline v5.2 after the submission to GenBank database of NCBI. CRISPR and genomic island were predicted using the CRISPR recognition tool (Bland et al. 2007) and IslandPath-DIMOB (Langille et al. 2008), respectively. In addition, calling with RepeatMasker (Bailly-Bechet et al. 2014) revealed a similar number of repetitive elements in the assemblies.The predicted gene sequence was annotated with Cluster of Orthologous Groups of proteins (COG) (Wang et al. 2019), Kyoto Encyclopedia of Genes and Genomes (KEGG) (Kanehisa et al. 2016), NCBI nonredundant protein (Nr) (Deng et al. 2006), Swiss-Prot (20115_0) (The UniProt Consortium 2015), and other functional databases via BLAST v2.2.29. Based on the comparison result from the Nr database, the software Blast2GO v2.5 performed additional functional annotation based on the Gene Ontology (GO) (release 20160907) database (Jones et al. 2014). The software hmmer v3.0 was used to annotate the genome with the database Pfam (27.0) (El-Gebali et al. 2019). In addition, the software hmmer was used to predict carbohydrate-active enzymes (CAZy) based on the database CAZy (Cantarel et al. 2009).The assembled contig sequence was aligned with the Nucleotide database to determine the chromosome type. The assembly generated a single circular chromosome with total size of 3,763,082 bp, G+C content of 41.36%, and gene number of 3,696 (Fig. 1). Furthermore, 81 transfer RNAs, 8 rRNAs, 5 noncoding RNA families, and 41 pseudogenes were predicted from the genome. The numbers of CRISPR sites and genomic islands were 10 and 7, respectively. The total length of repetitive sequence was 5,580 bp. In addition, 2,418, 2,024 and 2,870 genes were annotated using the GO, KEGG, and COG databases, respectively. In total, 3,317 genes were annotated with Pfam, 3,358 with Swiss-Prot, and 3,792 with Nr.Fig. 1. Graphical circular chromosome map of Bacillus altitudinis LZP02. The seven circles (outer to inner) represent forward genome size, strand coding sequences, reverse-strand coding sequences, repetitive sequences, transfer RNA (blue) and ribosomal RNA (purple), GC content, and GC skew.Download as PowerPointThe GO database analysis showed that 1,081 and 33 genes were associated with molecular function of binding and biological process of locomotion, respectively, which may be beneficial to its plant colonization (Zeng et al. 2020). The KEGG analysis predicted a large number of ABC transporters (134 genes) and two-component systems (105 genes) in B. altitudinis LZP02. Moreover, considerable numbers of genes involved in flagellar assembly (31 genes), which are important for cross-kingdom communication and microbe–plant interactions (Guo et al. 2020), were also found. According to the KEGG analysis, 175 genes were involved in the metabolism of a variety of amino acids. The results showed that many genes related to the growth of plants were identified in B. altitudinis LZP02. In total, there were 31 genes coding for chemotaxis protein which were related to the colonization of rice roots and enhanced plant growth (Wang et al. 2020). The most abundant COG category was "General function prediction only" (n = 420), followed by "Amino acid transport and metabolism" (n = 352) (Fig. 1). The Pfam annotation showed that three genes were associated with antibiotic biosynthesis. The Swiss-Prot database analysis showed that 10 genes were associated with siderophore biosynthesis and transport. There were as many as 137 genes identified with the CAZy database. Analysis of multiple databases confirmed that B. altitudinis LZP02 promoted plant growth through diverse mechanisms (Backer et al. 2018).In the NCBI genome database, based on average nucleotide identity, B. altitudinis LZP02 has the higher symmetric identity of>98% to two other strains that were completely sequenced (B. altitudinis DSM 26896 and B. altitudinis P10). In addition, based on digital DNA-DNA hybridizations, the symmetric identity was greater than 92% with these two strains (Supplementary Table S1). Therefore, their genome assembly statistics were summarized for comparison (Table 1). A phylogenetic tree was determined using the Genome BLAST Distance Phylogeny method (Supplementary Fig. S1). OrthoMCL software was used to classify the protein sequences predicted from the three strains. Statistical analysis of the specific gene families of the strain was conducted. Then, the genes were annotated with the Pfam database. Compared with DSM 26896 and P10, five unique gene families, including cytochrome P450, 50S ribosome-binding GTPase, RNA recognition motif, domain of unknown function, and protein of unknown function, only existed in the genome of B. altitudinis LZP02. The cytochrome P450 is important in the current agricultural systems (Dimaano and Iwakami 2021). Deoxynivalenol toxins from Fusarium graminearum could be degraded by cytochrome P450 (Ito et al. 2013). It also showed resistance to the herbicide bensulfuron methyI (Ohno et al. 2008). In addition, thus far, cytochrome P450 has not been reported in-depth in B. altitudinis species. Therefore, cytochrome P450 in B. altitudinis LZP02 may be helpful to plants, which is worthy of further study.Table 1. Genome assembly statistics of Bacillus altitudinis LZP02 and two strainsB. altitudinisParameterLZP02DSM 26896P10NCBI accessionCP075052.1JXAI00000000.1CP024204.1Genome size (bp)3,763,0823,812,5143,765,752GC content (%)41.5241.3041.36Number of protein-coding genes369638273679Number of ribosomal RNAs828Number of transfer RNAs813381Number of noncoding RNAs555Table 1. Genome assembly statistics of Bacillus altitudinis LZP02 and two strainsView as image HTML The annotation of bacterial chemotaxis pathways indicated that B. altitudinis LZP02 was capable of moving to beneficial plant rhizosphere exudates. A gene related to the formation of biofilms (bpuM) was found in the genome, and this gene was 82.28% similar to the gene luxS in B. subtilis 168 (sequence number NC_000964.3) (Yi et al. 2019). These results showed that B. altitudinis LZP02 has enhanced ability for the colonization in the plant rhizosphere with chemotaxis and biofilm formation. Many genes associated with acid stress resistance (pstS, glnQ, glnP, glnH, recN, pstB, and yybt) were found in B. altitudinis LZP02. We found the synthetic pathways of acetoin and 2,3-butanediol in B. altitudinis LZP02. This can shift carbohydrate catabolism from toxic compounds to neutral volatile compounds with growth-promoting ability (Guo et al. 2015). The pathway involves alsS and alsD, which encode acetolactate synthase and acetolactate decarboxylase, respectively; and alsR, which regulates these genes. In addition, we found some genes that encode arginine decarboxylase and agmatinase (speA and speB) in the B. altitudinis LZP02 genome. These genes may transform amino acids to plant-growth-promoting substances (Guo et al. 2015). In the B. altitudinis LZP02 genome, the genes for the transportation of metal ions (mgtE, mntH, and corA) were associated with the uptake of nutrients in the plant host (Guo et al. 2015) (Supplementary Table S2). Therefore, complete genome sequence data are essential for exploring the potential ability of the strain and the beneficial functions in plant–microbe interactions.The analysis of the genome showed that B. altitudinis LZP02 might promote plant growth through multiple mechanisms such as siderophore, bacterial chemotaxis, antibiotics production, resistance to acid stress, volatile compounds, and uptake of nutrients. In this study, the complete genome of the B. altitudinis LZP02 represents a valuable resource for the investigation of plant-growth-promoting functions and plant–microbe interactions.Data AvailabilityThe complete genome sequence of B. altitudinis LZP02 has been deposited in GenBank under the accession number CP075052. (BioProject: PRJNA728205, BioSample: SAMN19072201).The author(s) declare no conflict of interest.Literature CitedAkinrinlola, R., Adesemoye, A. O., and Yuen, G. Y. 2018. 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This is an open access article distributed under the CC BY-NC-ND 4.0 International license.DetailsFiguresLiterature CitedRelated Vol. 35, No. 5 May 2022ISSN:0894-0282e-ISSN:1943-7706 Download Metrics Downloaded 780 times Article History Issue Date: 13 May 2022Published: 13 Apr 2022Accepted: 10 Feb 2022 Pages: 428-431 InformationCopyright © 2022 The Author(s).This is an open access article distributed under the CC BY-NC-ND 4.0 International license.FundingNational Natural Science Foundation of ChinaGrant/Award Number: 31870493Key Research and Development Projects in Heilongjiang, ChinaGrant/Award Number: GA21B007Grant/Award Number: GZ20210067Basic Research Fees of Universities in Heilongjiang Province, ChinaGrant/Award Number: 135409103KeywordsBacillus altitudinisbacteria-plant symbiosisbiocontrolgenetics and gene regulationgenomegenomicsPGPRpromotes plant growthThe author(s) declare no conflict of interest.PDF download