Volume 18 Issue 3
Jun.  2022
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LIU Guangxin, DONG Yanjun, ZHAO Lijuan, DENG Yiqin, CHENG Changhong, MA Hongling, JIANG Jianjun, FENG Juan, GUO Zhixun, LIN Li. Sequencing of whole genome of Bacillus velezensis LG37 and screening of inorganic nitrogen metabolism candidate genes[J]. South China Fisheries Science, 2022, 18(3): 57-67. DOI: 10.12131/20210149
Citation: LIU Guangxin, DONG Yanjun, ZHAO Lijuan, DENG Yiqin, CHENG Changhong, MA Hongling, JIANG Jianjun, FENG Juan, GUO Zhixun, LIN Li. Sequencing of whole genome of Bacillus velezensis LG37 and screening of inorganic nitrogen metabolism candidate genes[J]. South China Fisheries Science, 2022, 18(3): 57-67. DOI: 10.12131/20210149
shu

Sequencing of whole genome of Bacillus velezensis LG37 and screening of inorganic nitrogen metabolism candidate genes

  • 1.

    South China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences/Key Laboratory of South China Sea Fishery Resources Exploitation & Utilization, Ministry of Agriculture and Rural Affairs, Guangzhou 510300, China

  • 2.

    Zhaoqing Fisheries Technology Extension Center, Zhaoqing 526040, China

  • 3.

    Zhongkai University of Agriculture and Engineering/Guangdong Provincial Water Environment and Aquatic Products Security Engineering Technology Research Center/Guangzhou Key Laboratory of Aquatic Animal Diseases and Waterfowl Breeding, Guangzhou 510225, China

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  • Received Date: May 19, 2021
  • Revised Date: July 06, 2021
  • Accepted Date: September 28, 2021
  • Available Online: October 18, 2021
    Graphical Abstract
    • Abstract
  • It has been found that Bacillus velezensis can assimilate inorganic nitrogen efficiently. However, the underlying mechanism of inorganic nitrogen assimilation remains enigmatic. In order to elucidate the mechanism, we sequenced the complete genome of LG37 by PacBio RS II and Illumina HiSeq 2000, and then annotated and analyzed the sequence by the database of NR, KEGG, eggNOG, GO and CARD. Finally, we screened the genes related to inorganic nitrogen metabolism by local Blast+. The results show that: 1) The genome contained one circular chromosomal with a size of 3 929 697 bp and a GC-content of 46.5%. Gene prediction and annotation was performed to acquire a total of 3 854 protein-coding genes, 86 tRNA genes and 27 rRNA genes. 2) A total of 94 inorganic nitrogen metabolism candidate genes were screened by local Blast+. These genes were involved into coding sensing protein, transcriptional regulator, transporter, oxidoreductase and assimilator, etc.. In conclusion, the whole genome sequencing and data analysis of LG37 provide data at gene level and theoretical basis for functional study and application of Bacillus in reducing inorganic nitrogen in aquaculture water.
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  • [1]
    胡晓娟, 文国樑, 田雅洁, 等. 不同培养条件下菌株NB5 对氨氮的去除效果研究[J]. 南方水产科学, 2020, 16(6): 89-96.
    [2]
    方金龙, 王元, 房文红, 等. 氨氮胁迫下白斑综合征病毒对凡纳滨对虾的致病性[J]. 南方水产科学, 2017, 13(4): 52-58. doi: 10.3969/j.issn.2095-0780.2017.04.007
    [3]
    肖炜, 李大宇, 徐杨, 等. 慢性氨氮胁迫对吉富罗非鱼幼鱼生长、免疫及代谢的影响[J]. 南方水产科学, 2015, 11(4): 81-87. doi: 10.3969/j.issn.2095-0780.2015.04.012
    [4]
    郭国强, 孙红飞, 张永耀. 分子氨对草鱼鱼种红细胞渗透脆性的影响[J]. 水产科学, 2010, 29(8): 489-491. doi: 10.3969/j.issn.1003-1111.2010.08.011
    [5]
    孙侦龙, 朱永祥, 刘大勇, 等. 非离子氨氮和亚硝酸盐氮对暗纹东方鲀稚鱼的急性毒性试验[J]. 水产科学, 2015, 34(3): 135-139.
    [6]
    KUEBUTORNYE F K A, ABARIKE E D, LU Y. A review on the application of Bacillus as probiotics in aquaculture[J]. Fish Shellfish Immunol, 2019, 87: 820-828. doi: 10.1016/j.fsi.2019.02.010
    [7]
    LIU G X, VIJAYARAMAN S B, DONG Y J, et al. Bacillus velezensis LG37: transcriptome profiling and functional verification of GlnK and MnrA in ammonia assimilation[J]. BMC Genom, 2020, 21(1): 215. doi: 10.1186/s12864-020-6621-1
    [8]
    GOODWIN S, MCPHERSON J D, MCCOMBIE W R. Coming of age: ten years of next-generation sequencing technologies[J]. Nat Rev Genet, 2016, 17(6): 333-51.
    [9]
    GALPERIN M Y, KRISTENSEN D M, MAKAROVA K S, et al. Microbial genome analysis: the COG approach[J]. Brief Bioinform, 2019, 20(4): 1063-1070. doi: 10.1093/bib/bbx117
    [10]
    CASTAÑEDA C D, GAMBLE J N, WAMSLEY K G S, et al. In ovo administration of Bacillus subtilis serotypes effect hatchability, 21-day performance, and intestinal microflora[J]. Poult Sci, 2021, 100(6): 101125. doi: 10.1016/j.psj.2021.101125
    [11]
    TAKAMI H, TOYODA A, UCHIYAMA I, et al. Complete genome sequence and expression profile of the commercial lytic enzyme producer Lysobacter enzymogenes M497-1[J]. DNA Res, 2017, 24(2): 169-177.
    [12]
    MOLTON J S, LEE I R, BERTRAND D, et al. Stool metagenome analysis of patients with Klebsiella pneumoniae liver abscess and their domestic partners[J]. Int J Infect Dis, 2021, 107: 1-4. doi: 10.1016/j.ijid.2021.04.012
    [13]
    朱玉玲, 彭晶, 唐诗哲, 等. 宏基因组技术在极端环境酯酶挖掘中的应用[J]. 生命科学研究, 2021, 25(2): 169-175.
    [14]
    魏大鹏, 单洪伟, 马甡, 等. 混料设计优化复合菌剂比例的研究[J]. 南方水产科学, 2014, 10(1): 86-91. doi: 10.3969/j.issn.2095-0780.2014.01.013
    [15]
    TAMURA K, STECHER G, PETERSON D, et al. MEGA6: molecular evolutionary genetics analysis version 6.0[J]. Mol Biol Evol, 2013, 30(12): 2725-2729. doi: 10.1093/molbev/mst197
    [16]
    NAKANO K, SHIROMA A, SHIMOJI M, et al. Advantages of genome sequencing by long-read sequencer using SMRT technology in medical area[J]. Hum Cell, 2017, 30(3): 149-161. doi: 10.1007/s13577-017-0168-8
    [17]
    GAN Y Q, ZHANG T, GAN Y Q, et al. Complete genome sequences of two Enterococcus faecium strains and comparative genomic analysis[J]. Exp Ther Med, 2020, 19(3): 2019-2028.
    [18]
    BENNETT J P Jr, KEENEY P M, BROHAWN D G. RNA sequencing reveals small and variable contributions of infectious agents to transcriptomes of postmortem nervous tissues from amyotrophic lateral sclerosis, Alzheimer's disease and Parkinson's disease subjects, and increased expression of genes from disease-activated microglia[J]. Front Neurosci, 2019, 13: 235. doi: 10.3389/fnins.2019.00235
    [19]
    EMSLEY C, KING S, NYULASI I, et al. A GLIMmer of insight into lung transplant nutrition: enhanced detection of malnutrition in lung transplant patients using the GLIM criteria[J]. Clin Nutr, 2021, 40(5): 2521-2526. doi: 10.1016/j.clnu.2021.02.047
    [20]
    CHAN P P, LOWE T M. tRNAscan-SE: searching for tRNA genes in genomic sequences[J]. Methods Mol Biol, 2019, 1962: 1-14.
    [21]
    LAGESEN K, HALLIN P, RØDLAND E A, et al. RNAmmer: consistent and rapid annotation of ribosomal RNA genes[J]. Nucleic Acids Res, 2007, 35(9): 3100-8. doi: 10.1093/nar/gkm160
    [22]
    CAMACHO C, COULOURIS G, AVAGYAN V, et al. BLAST+: architecture and applications[J]. BMC Bioinformatics, 2009, 10: 421. doi: 10.1186/1471-2105-10-421
    [23]
    NAYAK V S. Nonelectrolytic production of caustic soda and hydrochloric acid from sodium chloride[J]. Ind Eng Chem Res, 1996, 35(10): 3808-3811. doi: 10.1021/ie960043h
    [24]
    张静, 高婷婷, 李勇, 等. 蛋白营养对工业养殖大菱鲆 (Scophthatmus maximus L.)幼鱼生长、氨氮排泄及肌肉氨基酸的效应[J]. 渔业科学进展, 2016, 37(6): 34-41. doi: 10.11758/yykxjz.20151124001
    [25]
    EBELING J M, TIMMONS M B, BISOGNI J J. Engineering analysis of the stoichiometry of photoautotrophic, autotrophic, and heterotrophic removal of ammonia-nitrogen in aquaculture systems[J]. Aquaculture, 2006, 257(1/2/3/4): 346-358.
    [26]
    雷阳, 张倩, 陈钰, 等. 对虾养殖高效降解氨氮微生态菌的筛选与鉴定[J]. 福建农业科技, 2019(10): 16-20.
    [27]
    ZHU X H, ZHANG S M, ZHOU L Y, et al. Probiotic potential of Bacillus velezensis: antimicrobial activity against non-O1 Vibrio cholerae and immune enhancement effects on Macrobrachium nipponense[J]. Aquaculture, 2021, 541: 736817. doi: 10.1016/j.aquaculture.2021.736817
    [28]
    张德锋, 高艳侠, 可小丽, 等. 贝莱斯芽孢杆菌LF01基因组序列分析及其代谢产物的生防作用[J]. 水产学报, 2022, 46(2): 196-206.
    [29]
    FAN B, BLOM J, KLENK H P, et al. Bacillus amyloliquefaciens, Bacillus velezensis, and Bacillus siamensis form an "operational group B. amyloliquefaciens" within the B. subtilis species complex[J]. Front Microbiol, 2017, 8: 22.
    [30]
    MURUKE M S H, CAMP H J O D, SEMESI A K, et al. The level of enzymes involved in the allantoin metabolism of Bacillus fastidiosus grown under different conditions[J]. Curr Microbiol, 1995, 30(1): 45-7. doi: 10.1007/BF00294523
    [31]
    NIU T, LV X, LIU Z, et al. Synergetic engineering of central carbon and nitrogen metabolism for the production of N-acetylglucosamine in Bacillus subtilis[J]. Biotechnol Appl Biochem, 2020, 67(1): 123-132. doi: 10.1002/bab.1845
    [32]
    WANG B, ZHANG D, CHU S, et al. Genomic analysis of Bacillus megaterium NCT-2 reveals its genetic basis for the bioremediation of secondary salinization soil[J]. Int J Genomics, 2020, 2020: 4109186.
    [33]
    MASSAD R S, LOUBET B, TUZET A, et al. Relationship between ammonia stomatal compensation point and nitrogen metabolism in arable crops: current status of knowledge and potential modelling approaches[J]. Environ Pollut, 2008, 154(3): 390-403.
    [34]
    TANG Y, YE Z, WEI Y, et al. Vertebrate paralogous CRMPs in nervous system: evolutionary, structural, and functional interplay[J]. J Mol Neurosci, 2015, 55(2): 324-34. doi: 10.1007/s12031-014-0327-2
    [35]
    顾志良, 耿拓宇. 鸡重要性状主效基因和QTL 的研究进展[J]. 中国家禽, 2003(S1): 130-134.
    [36]
    AWADA H, THAPA B, VISCONTE V. The genomics of myelodysplastic syndromes: origins of disease evolution, biological pathways, and prognostic implications[J]. Cells, 2020, 9(11): 2512. doi: 10.3390/cells9112512
    [37]
    丁忠涛, 张锐, 郭三堆. 棉花抗逆相关基因GhDr1的克隆及生物信息学分析[J]. 生物技术通报, 2011(1): 99-106.
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