Polyphasic analysis reveals correlation between phenotypic and genotypic analysis in soybean bradyrhizobia (Bradyrhizobium spp.).
Polyphasic analysis reveals correlation between phenotypic and genotypic analysis in soybean bradyrhizobia (Bradyrhizobium spp.).
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DOI：
10.1016/j.syapm.2020.126073
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发表时间：
2020-05
影响因子：
3.4
通讯作者：
Fuhrmann JJ
中科院分区：
文献类型：
--
作者：
Joglekar P;Mesa CP;Richards VA;Polson SW;Wommack KE;Fuhrmann JJ
大豆缓生根瘤菌（缓生根瘤菌属）是一种将大气氮固定在大豆根瘤内的细菌，大豆是满足全球营养蛋白需求的关键作物。这一群体的成员在共生效果上有所不同，历史上表型和基因型方法都被用来评估慢生根瘤菌的多样性。然而，各种评估方法之间的一致性却鲜为人知。采用内转录间隔物限制性片段长度多态性（ITS-RFLP）、细胞脂肪酸组成（脂肪酸甲酯，FAME）和血清学反应对382株大豆慢生根瘤菌（日本慢生根瘤菌、重氮根瘤菌和elkanii根瘤菌）进行了鉴定，以评估表型和基因型方法之间的一致性。总的来说，76%的条目使用这两种技术表现出相同的聚类。FAME能够识别所有382例病例，而14%的血清学无反应。一个包含36个Delaware分离株的ITS- rflp组产生了多个ITS扩增子，表明它们具有多个核糖体RNA （rrn）操作子。克隆和测序显示，这些菌株含有多达三个异质rrn操纵子，这是以前在慢生根瘤菌中未知的特性。采用16S rRNA和ITS扩增子测序进一步对96株具有代表性的亚群进行了表征。ITS序列的种间和种内识别率（65 ~ 99%）高于16S序列（96 ~ 99%）。本研究表明，表型和基因型方法在物种或更高水平上密切相关，但应谨慎处理。我们还建议使用16S和ITS基因分型数据，以获得更好的种间和种内的慢生根瘤菌分类。
Soybean bradyrhizobia (Bradyrhizobium spp.) are bacteria that fix atmospheric nitrogen within the root nodules of soybean, a crop critical for meeting global nutritional protein demand. Members of this group differ in symbiotic effectiveness, and historically both phenotypic and genotypic approaches have been used to assess bradyrhizobial diversity. However, agreement between various approaches of assessment is poorly known. A collection (n=382) of soybean bradyrhizobia (Bradyrhizobium japonicum, B. diazoefficiens, and B. elkanii) were characterized by Internal Transcribed Spacer – Restriction Fragment Length Polymorphism (ITS-RFLP), cellular fatty acid composition (fatty acid methyl esters, FAME), and serological reactions to assess agreement between phenotypic and genotypic methods. Overall, 76% of the accessions demonstrated identical clustering with each of these techniques. FAME was able to identify all 382 accessions, whereas 14% were non-reactive serologically. One ITS-RFLP group, containing 36 Delaware isolates, produced multiple ITS amplicons indicating they possess multiple ribosomal RNA (rrn) operons. Cloning and sequencing revealed that these strains contained as many as three heterogenous rrn operons, a trait previously unknown in bradyrhizobia. A representative subset of 96 isolates was further characterized using 16S rRNA and Internal Transcribed Spacer (ITS) amplicon sequencing. ITS sequences showed better inter and intra-species discrimination (65–99% identity) than 16S sequences (96–99% identity). This study shows that phenotypic and genotypic approaches are strongly correlated at the species level or higher but should be approached with caution. We also suggest using combined 16S and ITS genotyping data to obtain better inter- and intra-species resolution in bradyrhizobia classification.
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影响因子：
3.5
作者：
Kaneko T;Maita H;Hirakawa H;Uchiike N;Minamisawa K;Watanabe A;Sato S
通讯作者：
Sato S
影响因子：
4.1
作者：
Kaneko, T;Nakamura, Y;Tabata, S
通讯作者：
Tabata, S
DOI：
10.1099/00207713-38-4-358
发表时间：
1988-10-01
期刊：
INTERNATIONAL JOURNAL OF SYSTEMATIC BACTERIOLOGY
影响因子：
--
作者：
KUYKENDALL, LD;ROY, MA;DEVINE, TE
通讯作者：
DEVINE, TE
影响因子：
3.4
作者：
Avontuur, Juanita R.;Palmer, Marike;Steenkamp, Emma T.
通讯作者：
Steenkamp, Emma T.
影响因子：
4.4
作者：
Azevedo, Helton;Lopes, Fabricio Martins;Hungria, Mariangela
通讯作者：
Hungria, Mariangela