College of Biological Science and Technology, Beijing Forestry University, Beijing 100083, China.
Department of Chemistry, MOE (Ministry of Education) Key Laboratory of Bioorganic Phosphorus Chemistry & Chemical Biology, Tsinghua University, Beijing 100084, China.
Int J Mol Sci. 2023 Aug 30;24(17):13449. doi: 10.3390/ijms241713449.
Plant endophytic bacteria play important roles in plants' growth and resistance to stress. It is important to characterize endophytic bacteria to be able to understand their benefits. Matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS) has become a powerful technique for bacterial identification due to its high throughput and simple procedures. In this study, the endophytic bacteria separated from (the leaves, roots and stems of Carrière; stems of Linn. var. ; and stems of Moench) were identified and classified based on MALDI-TOF MS data and 16S rRNA gene sequencing. The sampling and preparation of bacteria were optimized to obtain meaningful protein mass fingerprints. The composite correlation index (CCI) values of the inter-genera and inter-species protein mass fingerprints demonstrated sufficient differences between the strains. In the CCI value matrix for ten species in the same genus, all the CCI values were less than 0.5. Among the species, 95.6% of all the CCI values were less than 0.5. After data processing, the classification capacity of the protein mass fingerprints was verified using inter-specific and inter-generic PCoA. To compare different methods' potential for differentiation and phylogenetic analysis, a dendrogram of the MS profiles and a phylogenetic tree based on the 16S rRNA gene sequences were constructed using 61 endophytic bacteria found in . The clustering and grouping results show that the phylogenetic analysis based on MALDI-TOF MS is similar to that based on 16S rRNA gene sequencing. This study provides a valuable reference for differentiating and identifying endophytic bacteria according to their protein mass fingerprints.
植物内生细菌在植物生长和抵抗胁迫方面发挥着重要作用。对内生细菌进行特征描述以了解其益处是很重要的。基质辅助激光解吸电离飞行时间质谱（MALDI-TOF MS）由于其高通量和简单的程序，已成为一种强大的细菌鉴定技术。在这项研究中，根据 MALDI-TOF MS 数据和 16S rRNA 基因测序，对从（Carrière 的叶、根和茎；Linn. var. 的茎；和 Moench 的茎）中分离的内生细菌进行了鉴定和分类。优化了细菌的采样和制备，以获得有意义的蛋白质质量指纹图谱。属间和种间蛋白质质量指纹图谱的复合相关指数（CCI）值表明菌株之间存在足够的差异。在同一属的十种物种的 CCI 值矩阵中，所有 CCI 值均小于 0.5。在这些物种中，所有 CCI 值的 95.6%都小于 0.5。经过数据处理，使用种间和属间 PCoA 验证了蛋白质质量指纹图谱的分类能力。为了比较不同方法在分化和系统发育分析方面的潜力，使用在 中发现的 61 种内生细菌构建了 MS 图谱的系统发育树和基于 16S rRNA 基因序列的系统发育树。聚类和分组结果表明，基于 MALDI-TOF MS 的系统发育分析与基于 16S rRNA 基因测序的系统发育分析相似。这项研究为根据蛋白质质量指纹图谱区分和鉴定内生细菌提供了有价值的参考。
