Draft genome sequences of bacteria isolated from the Deschampsia antarctica phyllosphere
Draft genome sequences of bacteria isolated from the Deschampsia antarctica phyllosphere
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DOI：
10.1007/s00792-018-1015-x
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发表时间：
2018-05-01
期刊：
影响因子：
2.9
通讯作者：
Jorquera, Milko A.
中科院分区：
文献类型：
--
作者：
Cid, Fernanda P.;Maruyama, Fumito;Jorquera, Milko A.
基因组分析正被用于表征生活在不同植物隔室中的植物促生长（PGP）细菌。在这种情况下，我们最近从南极植物（Deschampsia anapartica）的叶际分离出的细菌显示冰重结晶抑制（IRI），抗冻蛋白（AFP）的存在相关的活动。在这项研究中，六个叶际细菌的基因组草案显示IRI活性的测序和注释，根据其功能基因类别。基因组大小范围从5.6到6.3 Mbp，并根据16 S rRNA基因的序列分析，5株被确定为假单胞菌属和一个作为Janthinobacterium。有趣的是，大多数菌株显示出与PGP性状相关的基因，如营养吸收（氨同化，固氮，磷酸酶和有机酸生产），生物活性代谢物（吲哚乙酸和1-氨基环丙烷-1-羧酸脱氨酶）和抗菌化合物（氰化氢和绿脓菌荧光素）。在与IRI活动，搜索推定的AFP使用当前的生物信息学工具也进行了。尽管在这些基因组中没有发现与报道的AFP相关的基因，但在所有假单胞菌菌株中发现了与冰核蛋白（InaA）相关的基因，但在Janthinobacterium菌株中没有发现。
Genome analyses are being used to characterize plant growth-promoting (PGP) bacteria living in different plant compartiments. In this context, we have recently isolated bacteria from the phyllosphere of an Antarctic plant (Deschampsia antarctica) showing ice recrystallization inhibition (IRI), an activity related to the presence of antifreeze proteins (AFPs). In this study, the draft genomes of six phyllospheric bacteria showing IRI activity were sequenced and annotated according to their functional gene categories. Genome sizes ranged from 5.6 to 6.3 Mbp, and based on sequence analysis of the 16S rRNA genes, five strains were identified as Pseudomonas and one as Janthinobacterium. Interestingly, most strains showed genes associated with PGP traits, such as nutrient uptake (ammonia assimilation, nitrogen fixing, phosphatases, and organic acid production), bioactive metabolites (indole acetic acid and 1-aminocyclopropane-1-carboxylate deaminase), and antimicrobial compounds (hydrogen cyanide and pyoverdine). In relation with IRI activity, a search of putative AFPs using current bioinformatic tools was also carried out. Despite that genes associated with reported AFPs were not found in these genomes, genes connected to ice-nucleation proteins (InaA) were found in all Pseudomonas strains, but not in the Janthinobacterium strain.