Differences in the Endophytic Microbiome of Olive Cultivars Infected by Xylella fastidiosa across Seasons
Abstract
:1. Introduction
2. Results
2.1. Description of the Microbiome by Whole Metagenome Shotgun Sequencing (WMSS)
2.2. Description of the Microbiome by 16S and ITS1 rRNA Gene Sequencing
2.3. Olive Xylem Microbiome Composition by WMSS Analysis
2.4. Olive Xylem Microbiome Composition by 16S and ITS1 rRNA Gene Analysis
2.5. Bacteria/Fungi Genera Shaping the Olive Xylem Microbiome
3. Discussion
4. Materials and Methods
4.1. Collection of Plant Samples
4.2. Extraction of Total DNA and Detection of Xylella Fastidiosa
4.3. Whole Metagenome Shotgun Sequencing and Bioinformatic Analysis
4.4. 16S and ITS1 rRNA Gene Library Sequencing and Bioinformatic Analysis
Supplementary Materials
Author Contributions
Funding
Acknowledgments
Conflicts of Interest
References
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Season | Cultivar | Sample Name * | Raw Total Reads * | Reads Classified * (%) | Reads Unclassified * (%) | Plants Reads ** (%) | Total Reads Microbes ** | Bacteria *** (%) | Fungi *** (%) | Archaea *** (%) | Viruses *** (%) | Xylella Cq | Xylella CFU/ml | % Xylella/Bacteria Reads | % Average Xylella/ Bacteria |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Spring April 2017 | FS17 | FS1-1 | 50,852,732 | 49,963,303 (98.2) | 889,429 (1.75) | 49,808,696 (99.69) | 259,160 | 249,675 (96.34) | 6893 (2.66) | 1735 (0.67) | 857 (0.33) | 28.30 | 34,100 | 0.37 | 2.32 |
FS1-3 | 46,489,102 | 45,588,956 (98.0) | 900,146 (1.94) | 45,428,720 (99.65) | 261,865 | 251,689 (96.11) | 7435 (2.84) | 1932 (0.74) | 809 (0.31) | 31.20 | 4430 | 0.06 | |||
FS1-10 | 52,171,471 | 51,356,470 (98.4) | 815,001 (1.56) | 51,202,008 (99.70) | 268,515 | 261,563 (97.41) | 4474 (1.67) | 1623 (0.60) | 855 (0.32) | 27.00 | 84,900 | 0.40 | |||
FS1-18 | 54,871,547 | 53,962,289 (98.3) | 909,258 (1.66) | 53,845,628 (99.78) | 205,545 | 198,322 (96.49) | 4550 (2.21) | 1801 (0.88) | 872 (0.42) | 30.10 | 9610 | 0.18 | |||
FS1-43 | 42,746,629 | 42,110,247 (98.5) | 636,382 (1.49) | 42,020,764 (99.79) | 158,999 | 154,117 (96.93) | 2764 (1.74) | 1277 (0.80) | 841 (0.53) | 22.90 | 1,520,000 | 12.87 | |||
FS1-45 | 39,194,825 | 38,375,168 (97.9) | 819,657 (2.09) | 38,227,260 (99.61) | 240,666 | 230,319 (95.70) | 7825 (3.25 | 1548 (0.64) | 974 (0.40) | 35.10 | 286 | 0.02 | |||
Kalamata | Kal1-53 | 38,656,227 | 38,101,308 (98.5) | 554,919 (1.44) | 38,028,096 (99.81) | 130,362 | 126,247 (96.84) | 2375 (1.82) | 980 (0.75) | 760 (0.58) | 36.10 | 142 | 0.05 | 8.69 | |
Kal1-54 | 44,921,146 | 43,839,640 (97.5) | 1,081,506 (2.41) | 43,586,856 (99.42) | 405,349 | 391,036 (96.47) | 11,283 (2.78) | 2135 (0.53) | 895 (0.22) | 28.50 | 29,600 | 0.10 | |||
Kal1-55 | 39,692,637 | 39,116,264 (98.5) | 576,373 (1.45) | 39,009,116 (99.73) | 178,457 | 172,754 (96.80) | 2438 (1.37) | 1077 (0.60) | 2188 (1.23) | 33.10 | 1170 | 0.02 | |||
Kal1-57 | 42,445,268 | 41,813,669 (98.5) | 631,599 (1.49) | 41,711,976 (99.76) | 181,331 | 176,926 (97.57) | 2647 (1.46) | 1203 (0.66) | 555 (0.31) | 31.10 | 4760 | 0.22 | |||
Kal1-65 | 45,136,293 | 44,493,779 (98.5) | 642,514 (1.42) | 44,384,016 (99.75) | 194,201 | 186,304 (95.93) | 2783 (1.43) | 4058 (2.09) | 1056 (0.54) | 34.10 | 577 | 0.04 | |||
Kal1-89 | 44,631,934 | 43,883,925 (98.3) | 748,009 (1.68) | 43,692,880 (99.56) | 343,522 | 337,244 (98.17) | 3490 (1.02) | 1417 (0.41) | 1371 (0.40) | 20.40 | 8,790,000 | 51.73 | |||
Autumn November 2018 | FS17 | FS2-1 | 33,462,404 | 32,788,919 (97.9) | 673,485 (2.01) | 32,749,304 (99.88) | 65,201 | 59,793 (91.71) | 3284 (5.04) | 989 (1.52) | 1135 (1.74) | 35.10 | 286 | 0.95 | 31.48 |
FS2-3 | 32,092,733 | 31,396,019 (97.8) | 696,714 (2.17) | 31,371,784 (99.92) | 38,374 | 34,366 (89.56) | 2222 (5.79) | 770 (2.01) | 1016 (2.65) | 29.96 | 10,600 | 4.89 | |||
FS2-10 | 33,465,333 | 32,683,674 (97.6) | 781,659 (2.34) | 32,631,210 (99.84) | 90,038 | 84,585 (93.94) | 3636 (4.04) | 934 (1.04) | 883 (0.98) | 25.50 | 244,000 | 46.82 | |||
FS2-18 | 32,789,969 | 32,080,877 (97.8) | 709,092 (2.16) | 32,029,304 (99.84) | 86,409 | 79,573 (92.09) | 4305 (4.98) | 957 (1.11) | 1574 (1.82) | 31.10 | 4760 | 15.42 | |||
FS2-43 | 42,453,647 | 41,659,140 (98.1) | 794,507 (1.87) | 41,142,644 (98.76) | 938,782 | 923,823 (98.41) | 10,798 (1.15) | 1082 (0.12) | 3079 (0.33) | 24.57 | 469,000 | 83.11 | |||
FS2-45 | 31,955,583 | 31,276,525 (97.8) | 679,058 (2.13) | 31,230,648 (99.85) | 77,562 | 72,841 (93.91) | 2862 (3.69) | 857 (1.10) | 1002 (1.29) | 26.60 | 112,000 | 37.68 | |||
Kalamata | Kal2-53 | 48,745,550 | 47,873,736 (98.2) | 871,814 (1.79) | 47,214,900 (98.62) | 1,198,439 | 1,188,286 (99.15) | 5768 (0.48) | 1299 (0.11) | 3086 (0.26) | 24.20 | 608,000 | 90.05 | 52.67 | |
Kal2-54 | 33,545,651 | 32,875,120 (98.0) | 670,531 (2.00) | 32,841,592 (99.90) | 56,343 | 51,642 (91.66) | 2265 (4.02) | 738 (1.31) | 1698 (3.01) | 21.50 | 4,060,000 | 34.41 | |||
Kal2-55 | 38,914,006 | 38,071,869 (97.8) | 842,137 (2.16) | 37,429,772 (98.31) | 1,162,983 | 1,152,955 (99.14) | 6234 (0.54) | 1318 (0.11) | 2476 (0.21) | 22.10 | 2,660,000 | 88.65 | |||
Kal2-57 | 30,275,514 | 29,663,797 (97.9) | 611,717 (2.02) | 29,635,620 (99.91) | 45,484 | 40,442 (88.91) | 2912 (6.40) | 902 (1.98) | 1228 (2.70) | 21.80 | 3,290,000 | 0.45 | |||
Kal2-65 | 29,620,002 | 29,066,308 (98.1) | 553,694 (1.87) | 29,033,788 (99.89) | 52,570 | 47,964 (91.24) | 2148 (4.09) | 771 (1.47) | 1687 (3.21) | 22.20 | 2,480,000 | 19.94 | |||
Kal2-89 | 25,255,482 | 24,756,720 (98.0) | 498,762 (1.97) | 24,597,096 (99.36) | 287,446 | 281,221 (97.83) | 2430 (0.85) | 729 (0.25) | 3066 (1.07) | 22.40 | 2,150,000 | 82.53 |
Season | Cv. | Sample Name | Total Raw Reads | Sequences Classified (%) | Sequences Unclassified (%) | Plant Sequences (%) | Bacteria (%) | Fungi (%) | % Xylella/ Bacteria | % Average Xylella/Bacteria | |||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
16S | ITS | 16S | ITS | 16S | ITS | 16S | |||||||
Spring April 2017 | FS17 | FS1-1 | 13,604 | 110,867 | 13,137 (96.6) | 88,348 (79.7) | 467 (3.4) | 22,519 (20.3) | 12,753 (97.1) | 384 (2.9) | 88,338 (100) | 0.8 | 10.3 |
FS1-3 | 14,415 | 25,801 | 13,859 (96.1) | 17,759 (68.8) | 556 (3.9) | 8042 (31.2) | 13,386 (96.6) | 473 (3.4) | 17,759 (100) | 0.4 | |||
FS1-10 | 14,930 | 77,958 | 14,440 (96.7) | 59,012 (75.7) | 490 (3.3) | 18,946 (24.3) | 14,253 (98.7) | 187 (1.3) | 59,012 (100) | 1.6 | |||
FS1-18 | 12,303 | 62,221 | 11,899 (96.7) | 31,172 (50.1) | 404 (3.3) | 31,049 (49.9) | 11,826 (99.4) | 73 (0.6) | 31,172 (100) | 2.7 | |||
FS1-43 | 10,505 | 64,245 | 10,259 (97.7) | 34,647 (53.9) | 246 (2.3) | 29,598 (46.1) | 10,125 (98.7) | 134 (1.3) | 34,647 (100) | 56.0 | |||
FS1-45 | 12,735 | 90,246 | 12,250 (96.2) | 63,942 (70.9) | 485 (3.8) | 26,304 (29.1) | 11,772 (96.1) | 478 (3.9) | 63,942 (100) | 0.0 | |||
Kalamata | Kal1-53 | 11,780 | 22,772 | 11,335 (96.2) | 15,618 (68.6) | 445 (3.8) | 7154 (31.4) | 11,296 (99.7) | 39 (0.3) | 15,618 (100) | 0.0 | 13.2 | |
Kal1-54 | 15,279 | 26,9041 | 14,598 (95.5) | 174,764 (65) | 681 (4.5) | 94,277 (35.0) | 13,807 (94.6) | 791 (5.4) | 174,761 (100) | 0.0 | |||
Kal1-55 | 12,827 | 26,740 | 12,407 (96.7) | 18,577 (69.5) | 420 (3.3) | 8163 (30.5) | 12,156 (98.0) | 251 (2.0) | 18,577 (100) | 0.0 | |||
Kal1-57 | 9529 | 18,716 | 9259 (97.2) | 12,313 (65.8) | 270 (2.8) | 6403 (34.2) | 9222 (99.6) | 37 (0.4) | 12,313 (100) | 0.0 | |||
Kal1-65 | 10,275 | 111,806 | 9936 (96.7) | 67,804 (60.6) | 339 (3.3) | 44,002 (39.4) | 9897 (99.6) | 39 (0.4) | 67,804 (100) | 0.0 | |||
Kal1-89 | 12,140 | 17,612 | 11,612 (95.7) | 15,966 (90.7) | 528 (4.3) | 16,746 (95.1) | 10,808 (93.1) | 804 (6.9) | 15,966 (100) | 79.2 | |||
Autumn November 2018 | FS17 | FS2-1 | 151,666 | 88,600 | 151,475 (99.9) | 78,642 (88.8) | 191 (0.1) | 9958 (11.2) | 15,1200 (99.8) | 275 (0.2) | 78,642 (100) | 0.0 | 20.5 |
FS2-3 | 246,844 | 209,701 | 246,317 (99.8) | 188,116 (89.7) | 527 (0.2) | 21,848 (10.4) | 246,201 (99.9) | 116 (0.05) | 187,853 (99.9) | 6.9 | |||
FS2-10 | 195,548 | 219,077 | 195,319 (99.9) | 203,699 (93.0) | 229 (0.1) | 15,975 (7.3) | 195,168 (99.9) | 150 (0.1) | 203,102 (99.7) | 46.0 | |||
FS2-18 | 175,303 | 91,227 | 175,011 (99.8) | 73,264 (80.3) | 292 (0.2) | 18,023 (19.8) | 174,853 (99.9) | 158 (0.1) | 73,204 (99.9) | 12.7 | |||
FS2-43 | 92,265 | 103,006 | 92,257 (100) | 97,801 (94.9) | 8 (0) | 5205 (5.1) | 92,062 (99.8) | 195 (0.2) | 97,801 (100) | 44.1 | |||
FS2-45 | 131,843 | 65,534 | 131,659 (99.9) | 23,987 (36.6) | 184 (0.1) | 41,709 (63.6) | 131,416 (99.8) | 243 (0.2) | 23,825 (99.3) | 13.2 | |||
Kalamata | Kal2-53 | 168,034 | 54,316 | 167,912 (99.9) | 23,089 (42.5) | 122 (0.1) | 31,227 (57.5) | 167,418 (99.7) | 494 (0.3) | 23,089 (100) | 77.9 | 45.0 | |
Kal2-54 | 243,771 | 69,589 | 243,266 (99.8) | 58,880 (84.6) | 505 (0.2) | 10,728 (15.4) | 243,189 (99.9) | 77 (0.03) | 58,861 (100) | 39.0 | |||
Kal2-55 | 121,959 | 199,625 | 121,878 (99.9) | 143,056 (71.7) | 81 (0.1) | 56,569 (28.3) | 121,179 (99.4) | 699 (0.6) | 143,056 (100) | 81.4 | |||
Kal2-57 | 162,670 | 47,373 | 162,263 (99.7) | 47,368 (100) | 407 (0.3) | 244 (0.5) | 162,224 (99.9) | 39 (0.02) | 47,129 (99.5) | 0.0 | |||
Kal2-65 | 69,232 | 78,285 | 69,182 (99.9) | 39,009 (49.8) | 50 (0.1) | 39,276 (50.2) | 69,143 (99.9) | 39 (0.1) | 39,009 (100) | 15.4 | |||
Kal2-89 | 155,471 | 84,249 | 155,407 (100) | 81,875 (97.2) | 64 (0) | 2374 (2.8) | 155,219 (99.9) | 188 (0.1) | 81,875 (100) | 56.4 |
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Giampetruzzi, A.; Baptista, P.; Morelli, M.; Cameirão, C.; Lino Neto, T.; Costa, D.; D’Attoma, G.; Abou Kubaa, R.; Altamura, G.; Saponari, M.; et al. Differences in the Endophytic Microbiome of Olive Cultivars Infected by Xylella fastidiosa across Seasons. Pathogens 2020, 9, 723. https://doi.org/10.3390/pathogens9090723
Giampetruzzi A, Baptista P, Morelli M, Cameirão C, Lino Neto T, Costa D, D’Attoma G, Abou Kubaa R, Altamura G, Saponari M, et al. Differences in the Endophytic Microbiome of Olive Cultivars Infected by Xylella fastidiosa across Seasons. Pathogens. 2020; 9(9):723. https://doi.org/10.3390/pathogens9090723
Chicago/Turabian StyleGiampetruzzi, Annalisa, Paula Baptista, Massimiliano Morelli, Cristina Cameirão, Teresa Lino Neto, Daniela Costa, Giusy D’Attoma, Raied Abou Kubaa, Giuseppe Altamura, Maria Saponari, and et al. 2020. "Differences in the Endophytic Microbiome of Olive Cultivars Infected by Xylella fastidiosa across Seasons" Pathogens 9, no. 9: 723. https://doi.org/10.3390/pathogens9090723