Identification and Classification of Rhizobia by Matrix-Assisted Laser Desorption/Ionization Time-Of-Flight Mass Spectrometry.
Mass spectrometry (MS) has been widely used for specific, sensitive and rapid analysis of proteins and has shown a high potential for bacterial identification and characterization. Type strains of four species of rhizobia andEscherichia coliDH5α were employed as reference bacteria to optimize various parameters for identification and classification of species of rhizobia by matrix-assisted laser desorption/ionization time-of-flight MS (MALDI TOF MS). The parameters optimized included culture medium states (liquid or solid), bacterial growth phases, colony storage temperature and duration, and protein data processing to enhance the bacterial identification resolution, accuracy and reliability. The medium state had little effects on the mass spectra of protein profiles. A suitable sampling time was between the exponential phase and the stationary phase. Consistent protein mass spectral profiles were observed forE. colicolonies pre-grown for 14 days and rhizobia for 21 days at 4°C or 21°C. A dendrogram of 75 rhizobial strains of 4 genera was constructed based on MALDI TOF mass spectra and the topological patterns agreed well with those in the 16S rDNA phylogenetic tree. The potential of developing a mass spectral database for all rhizobia species was assessed with blind samples. The entire process from sample preparation to accurate identification and classification of species required approximately one hour.
Department of Molecular Biosciences and Bioengineering, University of Hawaii at Manoa, Honolulu, HI 96822, USA ; State Key Laboratory of Agro biotechnology, College of Biological Sciences, China Agricultural University, Beijing, 100193, China ; State Key Biotechnology Laboratory for Tropical Crops, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agriculture Sciences, Haikou, Hainan, 571101, China.
Rui Zong
RZ
Jia
State Key Laboratory of Agro biotechnology, College of Biological Sciences, China Agricultural University, Beijing, 100193, China ; Dongying Municipal Bureau of Agriculture, Dongying, Shandong, 257091, China.
Rong Juan
RJ
Zhang
State Key Laboratory of Agro biotechnology, College of Biological Sciences, China Agricultural University, Beijing, 100193, China ; State Key Biotechnology Laboratory for Tropical Crops, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agriculture Sciences, Haikou, Hainan, 571101, China.
Qing
Q
Wei
Department of Molecular Biosciences and Bioengineering, University of Hawaii at Manoa, Honolulu, HI 96822, USA ; State Key Laboratory of Agro biotechnology, College of Biological Sciences, China Agricultural University, Beijing, 100193, China.
Wen Feng
WF
Chen
Department of Molecular Biosciences and Bioengineering, University of Hawaii at Manoa, Honolulu, HI 96822, USA.
Il Kyu
IK
Cho
State Key Laboratory of Agro biotechnology, College of Biological Sciences, China Agricultural University, Beijing, 100193, China.
Wen Xin
WX
Chen
Department of Molecular Biosciences and Bioengineering, University of Hawaii at Manoa, Honolulu, HI 96822, USA.
Qing X
QX
Li
Bacterial classification; Bacterial identification; MALDI TOF MS; Rhizobium