Differentiation of Closely Related Oak-Associated Gram-Negative Bacteria by Label-Free Surface Enhanced Raman Spectroscopy (SERS)
Abstract
:1. Introduction
2. Materials and Methods
2.1. Morphological, Physiological and Biochemical Analysis
2.1.1. Colony Morphology
2.1.2. Biofilm Formation
2.1.3. Carbohydrate Use
2.1.4. Antibiotic Susceptibility
2.2. SERS Analysis
2.2.1. Experimental Set Up for SERS Spectra Acquisition
2.2.2. SERS Substrate Preparation
2.2.3. Bacteria Sample Preparation for SERS
2.2.4. SERS Spectra Acquisition
2.2.5. Multivariate Cluster Analyses
3. Results
3.1. Morphological, Physiological and Biochemical Analysis
3.2. SERS Analysis
3.2.1. Structural Analysis Based on SERS Spectra
3.2.2. Differentiation via Multivariate Cluster Analyses
4. Discussion
5. Conclusions
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Data Availability Statement
Acknowledgments
Conflicts of Interest
References
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Tree | Site (GPS Coordinates) | Isolate Identification No. |
---|---|---|
Alfa (α) | 55.829832, 26.217380 | 21, 27, 30, 32, 33, 33.1,34, 36, 40, 46.1, 46.2, 49 |
Bravo (β) | 55.8301132, 26.2168633 | 24, 29, 35, 37, 47.1, 47.2 |
Isolate Identification Code | Colony Morphology | Morphotype | Closest NCBI Match, Accession No., % Identity |
---|---|---|---|
21, 33.1, 35 | Colonies are circular, flat with a slightly undulate margin, smooth and glistening, off-white with a grey bull’s eye in the center, translucent and mucoid. | A | Paenibacillus tundrae A10b, NR_044525.1, 99.32–99.46% |
27, 30, 34 | Colonies are circular, flat, cream colored, translucent, smooth and glistening, butyrous, the margin is entire. Changes LB agar medium color to bright yellow. A small spindle formation can be observed at the center of the colony with 40× magnification. | B | Pantoea agglomerans DSM 3493, NR_041978.1, 99.64–99.97% |
24, 29 | Colonies are circular, raised, buff color, glistening and butyrous, the center of the colony is rough, and the edges are smooth, the margin is entire. The colonies change color of LB agar medium to bright yellow. | C | Pseudomonas brenneri CFML 97–391, NR_025103.1, 99.86%; Pseudomonas proteolytica CMS 64, NR_025588.1, 99.59% |
32, 33, 36, 37, 40, 46.1, 46.2, 47.1, 47.2, 49 | Colonies are circular, flat, cream colored, translucent, smooth and glistening, butyrous, the margin is entire. Changes LB agar medium color to bright yellow. | D | Pseudomonas azotoformans NBRC 12693, NR_113600.1, 99.66–99.79% |
Morphotype | Isolate Identification No. | Average Diameter ± SD, µm | Biofilm Production | Antibiotic Disk Diffusion Test | Carbohydrate Use | |||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
AM-10 | CTX-30 | C-30 | K-30 | STP-10 | TIC-75 | L | M | Su | G | F | ||||
A | 21 | 0.444 ± 0.03 | − | S | R | S | S | R | R | Ac | Ac | Ac | Ac | Ac |
33.1 | 0.361 ± 0.039 | − | S | R | S | S | R | R | Ac | Ac | Ac | Ac | Ac | |
35 | 0.43 ± 0.042 | − | S | R | S | S | R | R | Ac | Ac | Ac | Ac | Ac | |
B | 27 | 0.324 ± 0.041 | − | S | S | S | S | S | R | Ac | Ac | Ac | Ac | Ac |
30 | 0.352 ± 0.04 | − | S | S | S | S | S | R | Ac | Ac | Ac | Ac | Ac | |
34 | 0.438 ± 0.028 | − | S | S | S | S | S | R | Ac | Ac | Ac | Ac | Ac | |
C | 24 | 0.326 ± 0.033 | moderate | R | R | R | S | R | R | − | − | − | Ac | − |
29 | 0.284 ± 0.014 | moderate | R | R | R | S | R | R | − | − | − | Ac | − | |
D | 32 | 0.366 ± 0.021 | − | R | R | R | S | R | R | − | − | − | Ac | − |
33 | 0.338 ± 0.03 | − | R | R | R | S | R | R | − | − | − | Ac | − | |
36 | 0.447 ± 0.047 | − | R | R | R | S | R | R | − | − | − | Ac | − | |
37 | 0.34 ± 0.023 | − | R | R | R | S | R | R | − | − | − | Ac | − | |
40 | 0.427 ± 0.037 | − | R | R | R | S | R | R | − | − | − | Ac | − | |
46.1 | 0.426 ± 0.036 | − | R | R | R | S | R | R | − | − | − | Ac | − | |
46.2 | 0.338 ± 0.028 | − | R | R | R | S | R | R | − | − | − | Ac | − | |
47.1 | 0.43 ± 0.073 | − | R | R | R | S | R | R | − | − | − | Ac | − | |
47.2 | 0.45 ± 0.042 | − | R | R | R | S | R | R | − | − | − | Ac | − | |
49 | 0.405 ± 0.042 | − | R | R | R | S | R | R | − | − | − | Ac | − |
Peak Wavenumber, cm−1 | Tentative Band Assignments * | |||||||
---|---|---|---|---|---|---|---|---|
24 | 27 | 30 | 33.1 | 34 | 35 | 37 | 49 | |
563.38 | T, G [10,54] | |||||||
574.21 | 573.52 | 573.01 | 573.47 | 572.08 | 573.63 | 573.57 | Deformation of C=O–C in lipids [55] or Trp [54,56,57] or carbohydrates [58] | |
621.65 | 625.66 | 622.17 | 623.31 | 620.93 | 622.5 | 622.03 | C–C twisting mode of Phe ring [7,10,29,54,56] | |
658.43 | 657.8 | 658.53 | 657.42 | 657.71 | 657.09 | 657.93 | 658.28 | G, ring breathing mode [9,59,60,61] or amino acids COO–[62] |
688.19 | 689.83 | 689.18 | 689.93 | 692.23 | C–S stretch [26,57] or Gly [54] | |||
739.19 | 727.8 | 737.96 | 733.83 | 737.14 | 734.21 | 738.08 | 737.93 | A, glycosidic ring breathing [9,10,15,26,63,64] |
807.14 | 804.25 | 804.8 | 805.45 | 807.23 | 801.95 | 804.72 | O–P–O [1,26] or C–N stretch [20] | |
836.42 | 832.58 | 831.81 | 830.52 | 832.87 | O–P–O stretching in T [10,59] or Tyr [29,59] | |||
859.65 | 858 | 858 | 859.14 | 859.65 | 858.69 | Phosphodiester, deoxyribose related to T [4,10] or Tyr [29] | ||
882.32 | 879.93 | 882.2 | 880.81 | T, ring bending [10], stretching of C–N or C–O–N or deformation of C–C–H [65] | ||||
922.65 | 919.72 | 922.49 | 920.2 | 922.4 | 922.32 | 922.51 | 922.53 | C–COO– stretch in carbohydrates [26,66] |
958.79 | 959.67 | 957.92 | 958.24 | 958.22 | C–N stretching [7,10,29,67] or C–C/C–O stretching in membrane proteins [10] | |||
966.22 | C–N stretch [26] or C=C deformation in G [61] | |||||||
1005.6 | Phe [7,10,29] | |||||||
1011.9 | 1009.1 | 1009.5 | 1010 | 1009.6 | 1009.5 | 1009.4 | Phe [68,69] or Trp [54,57] | |
1051 | 1050.3 | 1050.6 | 1050.9 | 1050.8 | 1051.1 | 1050.4 | 1050 | Phenylalanine (the in-plane C–H bending mode) [69] or stretching of C–O/CH2–OH in lipids [70] |
1091.2 | 1094.7 | 1099.2 | 1089.9 | PO2- of nucleic acid stretching [10,20,29] or deformation in carbohydrates(C–C, C–O, –COH) [7,65,67] | ||||
1116.4 | 1119.2 | Trp [65] | ||||||
1131.1 | 1129.6 | C–N and C–C stretching in carbohydrates [61,69] or =C–C= in unsaturated fatty acids in lipids [16,29] | ||||||
1159.3 | 1161.7 | 1159.8 | 1158.5 | 1158.5 | 1159.6 | 1158.3 | 1158.7 | C–C/C–N stretching in proteins [10] or carotenoids [15,29] |
1202 | 1201.9 | 1203 | 1200.8 | 1201.5 | 1201.6 | 1201.1 | 1201.7 | =C–C= in lipids [69] or aromatic amino acids in proteins [71] |
1247.2 | 1247.4 | 1247.6 | 1246.4 | 1254.8 | 1250.9 | 1252.5 | 1256.9 | Amide III [10,26,29,62,65] |
1301.4 | 1301.7 | 1303.1 | 1301.6 | 1300.4 | CH2 twist in lipids [10,55] | |||
1328.4 | 1325.2 | 1327.7 | 1328.2 | 1328.5 | 1328 | 1327.4 | 1327.3 | A [9,62,63,70,72] |
1363.7 | 1363.3 | 1363.5 | 1363.8 | 1363.8 | 1364.7 | 1366.4 | Trp [10] or C–H deformation in proteins/COO– deformation [5,73] | |
1383 | 1387.1 | 1388.8 | 1386.3 | COO– stretching in proteins [66,74] or CH3 bending [29] | ||||
1398.8 | COO– symmetric stretching [1,75] or deformation of CH3 [76] | |||||||
1421.2 | CH2 deformation in lipids [50,66,68] or A, G [66,71] | |||||||
1470.4 | 1467.8 | 1469.6 | 1470 | 1470 | 1470.2 | 1469.6 | 1468.8 | Lipids [9,10] or deformation of C–H in proteins [65,69] |
1501.2 | Fatty acids in lipids [5,73] or carotenoids [29] or amino acids [74] | |||||||
1511.1 | 1511.5 | Carotenoids [29,77] or Phe [70] | ||||||
1569.4 | 1570.5 | 1570.1 | 1570.9 | 1569.9 | 1569.5 | 1569.3 | Tyr/proteins [69,70] or A/G [78] | |
1592.4 | Proteins [10] or A/G [1,7] or Tyr [72,79] | |||||||
1634.5 | 1634.7 | 1636.8 | 1634.5 | 1635.5 | 1633.1 | 1633 | Amide I in lipids [10,26,72] | |
1647.9 | Amide I [69] or T [29,68] | |||||||
1679.2 | 1694 | 1681.1 | 1684.3 | 1676.6 | 1682.8 | Amide I [10,62,71,75] | ||
1703.4 | C=O [5,71] | |||||||
1750.2 | C=O stretching [5,21] |
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Vaitiekūnaitė, D.; Snitka, V. Differentiation of Closely Related Oak-Associated Gram-Negative Bacteria by Label-Free Surface Enhanced Raman Spectroscopy (SERS). Microorganisms 2021, 9, 1969. https://doi.org/10.3390/microorganisms9091969
Vaitiekūnaitė D, Snitka V. Differentiation of Closely Related Oak-Associated Gram-Negative Bacteria by Label-Free Surface Enhanced Raman Spectroscopy (SERS). Microorganisms. 2021; 9(9):1969. https://doi.org/10.3390/microorganisms9091969
Chicago/Turabian StyleVaitiekūnaitė, Dorotėja, and Valentinas Snitka. 2021. "Differentiation of Closely Related Oak-Associated Gram-Negative Bacteria by Label-Free Surface Enhanced Raman Spectroscopy (SERS)" Microorganisms 9, no. 9: 1969. https://doi.org/10.3390/microorganisms9091969