Cover Crop Diversity as a Tool to Mitigate Vine Decline and Reduce Pathogens in Vineyard Soils
Abstract
:1. Introduction
2. Materials and Methods
2.1. Establishment of Experiments
2.2. Effect of Cover Crop Diversity on Disease Symptoms
2.3. Location and Greenhouse Conditions
2.4. Soil
2.5. Pathogen Incubation and Inoculation
2.6. Germination and Growth of Plants
2.7. Incidence of Disease
2.8. Molecular Data
2.9. DNA Extraction
2.10. Droplet Digital Assay
2.11. Illumina Sequencing and Bioinformatics
2.12. Statistical Analyses
3. Results
3.1. Cover Crop Growth
3.2. Effect of Cover Crops on Incidence of Disease in Vines
3.3. Recovery of Ilyonectria from Soil
3.4. Recovery of Ilyonectria from Roots
3.5. Sequence Results
3.6. Effect of Cover Crops on Fungal Diversity
3.6.1. Alpha Diversity
3.6.2. Beta Diversity in Native and Cultivar Studies
4. Discussion
4.1. Effect of Cover Crop Diversity on Root Necrosis
4.2. Effect of Cover Crop Diversity on Abundance of Ilyonectria
4.3. Effect of Cover Crop Diversity on Fungal Diversity
4.4. Effect of Cover Crops on Community Composition
5. Conclusions
Author Contributions
Funding
Acknowledgments
Conflicts of Interest
Appendix A
Site Properties | Response |
---|---|
Fruit tree | Sweet cherry |
Soil texture | Loamy sand |
pH | 6.9 |
Organic matter (%) | 2.3 |
C/N ratio | 8.5 |
Phosphorous (ppm) | 66 |
Potassium (ppm) | 360 |
Magnesium (ppm) | 170 |
Calcium (ppm) | 1330 |
Sodium (ppm) | 25 |
Aluminum (ppm) | 13 |
Sulfur (ppm) | 9 |
Nitrate (ppm) | 23 |
Date | Fertilizer Type | Amount Applied | Dilution |
---|---|---|---|
October 11 2018 | 15-15-18 | 150 mL | 50% |
October 25 2018 | 15-15-18 | 150 mL | No |
November 1 2018 | 15-15-18 | 150 mL | 50% |
November 22 2018 | 15-15-18 | 150 mL | 33% |
November 29 2018 | 15-15-18 | 150 mL | 40% |
December 7 2018 | 15-15-18 | 150 mL | 40% |
Sample | Input | filtered | DenoisedF | DenoisedR | Merged | Nonchim |
---|---|---|---|---|---|---|
B1-1 | 12,251 | 6665 | 6644 | 6644 | 6184 | 6176 |
B1-10 | 14,589 | 8155 | 8133 | 8127 | 7909 | 7907 |
B1-14 | 14,193 | 8257 | 8222 | 8183 | 7307 | 7290 |
B1-15 | 16,920 | 9042 | 9020 | 9013 | 8424 | 8409 |
B1-16 | 16,354 | 8844 | 8808 | 8789 | 8057 | 8053 |
B1-20 | 21,936 | 9842 | 9807 | 9799 | 9040 | 9028 |
B1-3 | 9439 | 4599 | 4589 | 4590 | 4276 | 4268 |
B1-4 | 13,175 | 6559 | 6524 | 6520 | 6091 | 6086 |
B1-6 | 10,873 | 6568 | 6514 | 6530 | 5964 | 5962 |
B1-7 | 10,950 | 6140 | 6113 | 6094 | 5469 | 5451 |
B10-14 | 6011 | 3446 | 3429 | 3431 | 3150 | 3146 |
B10-16 | 13,831 | 7968 | 7941 | 7918 | 7248 | 7233 |
B10-17 | 10,982 | 4927 | 4898 | 4896 | 4548 | 4506 |
B10-18 | 10,059 | 5622 | 5605 | 5607 | 5053 | 5029 |
B10-19 | 12,876 | 7437 | 7419 | 7397 | 6604 | 6579 |
B10-22 | 21,342 | 11,584 | 11,551 | 11,564 | 10,118 | 10,041 |
B10-6 | 29,911 | 15,434 | 15,381 | 15,404 | 14,299 | 14,200 |
B10-7 | 8427 | 4811 | 4787 | 4784 | 4364 | 4352 |
B10-9 | 13,366 | 6560 | 6530 | 6534 | 5964 | 5957 |
B10-fal | 24,131 | 12,374 | 12,348 | 12,349 | 11,735 | 11,671 |
B2-1 | 12,412 | 6563 | 6522 | 6512 | 6117 | 6079 |
B2-10 | 19,272 | 11,002 | 10,973 | 10,965 | 10,166 | 10,161 |
B2-11 | 8626 | 4766 | 4754 | 4751 | 4461 | 4400 |
B2-12 | 17,980 | 9804 | 9768 | 9770 | 8801 | 8729 |
B2-13 | 10,050 | 5568 | 5552 | 5539 | 5178 | 5158 |
B2-17 | 18,591 | 10,111 | 10,080 | 10,067 | 8978 | 8935 |
B2-18 | 6488 | 3754 | 3734 | 3735 | 3644 | 3640 |
B2-21 | 20,710 | 10,897 | 10,864 | 10,863 | 10,170 | 10,086 |
B2-22 | 20,429 | 10,227 | 10,190 | 10,178 | 9386 | 9305 |
B2-5 | 12,175 | 7021 | 6998 | 6981 | 6355 | 6338 |
B2-9 | 15,943 | 8738 | 8696 | 8686 | 8171 | 8105 |
B3-1 | 14,605 | 8041 | 8015 | 8012 | 7281 | 7259 |
B3-13 | 8386 | 4782 | 4765 | 4758 | 4303 | 4296 |
B3-14 | 17,549 | 7704 | 7666 | 7648 | 7118 | 7107 |
B3-15 | 13,922 | 5942 | 5919 | 5924 | 5398 | 5398 |
B3-17 | 7866 | 4491 | 4473 | 4469 | 4090 | 4069 |
B3-2 | 22,018 | 11,332 | 11,274 | 11,270 | 10,318 | 10,247 |
B3-20 | 19,794 | 10,473 | 10,436 | 10,427 | 9681 | 9618 |
B3-21 | 24,717 | 12,958 | 12,908 | 12,923 | 12,068 | 11,915 |
B3-22 | 19,204 | 10,218 | 10,182 | 10,191 | 9640 | 9581 |
B3-3 | 6693 | 3643 | 3631 | 3622 | 3322 | 3316 |
B3-7 | 20,743 | 10,079 | 10,010 | 10,007 | 9315 | 9237 |
B3-fal | 18,855 | 10,320 | 10,296 | 10,251 | 9587 | 9503 |
B4-11 | 10,411 | 6031 | 6007 | 5994 | 5049 | 5049 |
B4-12 | 14,153 | 7003 | 6958 | 6956 | 6417 | 6403 |
B4-15 | 16,611 | 8708 | 8658 | 8662 | 7915 | 7840 |
B4-16 | 19,340 | 10,285 | 10,240 | 10,241 | 9650 | 9558 |
B4-18 | 8515 | 5131 | 5124 | 5122 | 4708 | 4697 |
B4-2 | 25,973 | 13,688 | 13,617 | 13,625 | 12,315 | 12,203 |
B4-21 | 23,882 | 12,563 | 12,498 | 12,473 | 11,638 | 11,530 |
B4-5 | 23,443 | 12,027 | 11,955 | 11,961 | 11,003 | 10,927 |
B4-7 | 20,209 | 10,317 | 10,270 | 10,265 | 9600 | 9531 |
B5-10 | 12,457 | 6726 | 6689 | 6707 | 6415 | 6378 |
B5-11 | 35,399 | 18,215 | 18,142 | 18,138 | 16,671 | 16,523 |
B5-12 | 24,203 | 13,410 | 13,350 | 13,349 | 12,385 | 12,216 |
B5-13 | 23,829 | 12,481 | 12,429 | 12,414 | 11,449 | 11,327 |
B5-15 | 29,538 | 17,066 | 17,035 | 17,022 | 16,486 | 16,416 |
B5-4 | 23,032 | 9630 | 9594 | 9580 | 8953 | 8943 |
B5-6 | 7570 | 3983 | 3967 | 3965 | 3565 | 3562 |
B5-9 | 11,398 | 4582 | 4558 | 4557 | 4269 | 4268 |
B6-11 | 11,204 | 6595 | 6572 | 6555 | 6071 | 6052 |
B6-12 | 8155 | 4512 | 4484 | 4491 | 4028 | 4021 |
B6-13 | 10,779 | 5783 | 5755 | 5744 | 5194 | 5178 |
B6-19 | 29,866 | 16,427 | 16,367 | 16,360 | 15,012 | 14,867 |
B6-2 | 17,688 | 9582 | 9411 | 9366 | 8683 | 8677 |
B6-20 | 8519 | 4795 | 4783 | 4782 | 4331 | 4317 |
B6-21 | 22,819 | 12,354 | 12,305 | 12,295 | 11,632 | 11,567 |
B6-3 | 5341 | 2866 | 2855 | 2851 | 2574 | 2573 |
B6-4 | 6254 | 847 | 832 | 835 | 771 | 769 |
B6-5 | 5377 | 2209 | 2198 | 2187 | 2000 | 1995 |
B7-1 | 24,124 | 12,565 | 12,508 | 12,504 | 11,635 | 11,547 |
B7-10 | 25,220 | 13,851 | 13,789 | 13,798 | 13,062 | 12,847 |
B7-11 | 9586 | 5557 | 5530 | 5516 | 5131 | 5111 |
B7-15 | 26,469 | 14,189 | 14,156 | 14,150 | 13,580 | 13,489 |
B7-17 | 16,917 | 8897 | 8856 | 8842 | 8204 | 8161 |
B7-19 | 13,208 | 8050 | 7998 | 7990 | 7187 | 7167 |
B7-20 | 10,609 | 6169 | 6151 | 6140 | 5595 | 5589 |
B7-22 | 29,654 | 16,540 | 16,492 | 16,503 | 15,391 | 15,259 |
B7-3 | 19,382 | 10,255 | 10,220 | 10,216 | 9450 | 9450 |
B7-5 | 11,105 | 5371 | 5353 | 5342 | 4865 | 4863 |
B7-7 | 12,032 | 6861 | 6824 | 6819 | 6298 | 6291 |
B7-fal | 24,746 | 13,168 | 13,147 | 13116 | 12,135 | 12,111 |
B8-12 | 20,947 | 10,878 | 10,833 | 10,825 | 9907 | 9825 |
B8-13 | 14,151 | 7813 | 7771 | 7781 | 7010 | 7009 |
B8-18 | 13,899 | 6928 | 6888 | 6886 | 6373 | 6342 |
B8-2 | 26,482 | 14,400 | 14,337 | 14,317 | 13,350 | 13,228 |
B8-20 | 18,913 | 9475 | 9447 | 9451 | 8770 | 8695 |
B8-21 | 14,129 | 7922 | 7901 | 7893 | 7391 | 7332 |
B8-22 | 18,843 | 9856 | 9801 | 9807 | 9007 | 8966 |
B8-5 | 20,503 | 10,688 | 10,648 | 10,648 | 10,081 | 10,023 |
B8-6 | 13,991 | 7014 | 6976 | 6985 | 6394 | 6378 |
B8-fal | 4603 | 2518 | 2478 | 2466 | 2362 | 2358 |
B9-10 | 11,953 | 5229 | 5209 | 5202 | 4679 | 4670 |
B9-14 | 6549 | 3955 | 3938 | 3941 | 3602 | 3599 |
B9-16 | 11,558 | 6775 | 6752 | 6755 | 6119 | 6111 |
B9-19 | 11,146 | 5144 | 5116 | 5115 | 4804 | 4744 |
B9-3 | 10,354 | 4664 | 4648 | 4644 | 4081 | 4076 |
B9-4 | 13,701 | 6974 | 6945 | 6933 | 6440 | 6422 |
B9-6 | 9487 | 4444 | 4414 | 4411 | 4093 | 4089 |
B9-9 | 19,158 | 10,136 | 10,094 | 10,088 | 9287 | 9246 |
B9-fal | 7037 | 4131 | 4117 | 4116 | 3850 | 3836 |
PRE-1 | 9227 | 5446 | 5423 | 5416 | 4963 | 4954 |
PRE-10 | 41,280 | 20,182 | 20,115 | 20,095 | 18,033 | 17,904 |
PRE-2 | 10,046 | 5575 | 5566 | 5559 | 5085 | 5084 |
PRE-3 | 16,164 | 7724 | 7665 | 7679 | 7081 | 7074 |
PRE-4 | 25,025 | 11,935 | 11,915 | 11,903 | 11,141 | 11,055 |
PRE-5 | 21,858 | 11,157 | 11,125 | 11,117 | 10,273 | 10,187 |
PRE-6 | 31,867 | 17,222 | 17,163 | 17,145 | 15,889 | 15,758 |
PRE-7 | 29,499 | 14,842 | 14,816 | 14,809 | 13,730 | 13,649 |
PRE-8 | 17,772 | 9465 | 9443 | 9436 | 8714 | 8689 |
PRE-9 | 22,917 | 12,095 | 12,053 | 12,062 | 11,220 | 11,125 |
Experiment | Cover Crop Treatment | Below-Ground Biomass | Above-Ground Biomass |
---|---|---|---|
Native study | All native | 0.885 a | 2.715 a |
Bluebunch | 0.795 a | 3.041 a | |
Lupine | 0.319 b | 0.730 b | |
Rockcress | 0.138 b | 1.380 b | |
Yarrow | 1.056 a | 2.822 a | |
Cultivar study | All cultivar | 1.238 a | 6.917 a |
Buckwheat | 0.694 b | 4.771 b | |
Clover | 0.527 b | 7.483 a | |
Mustard | 0.121 c | 1.834 c | |
Wheat | 2.272 d | 3.663 d |
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Treatment | Latin Binomial | Study | Diversity | Group | Life Cycle |
---|---|---|---|---|---|
Crimson clover | Trifolium incarnatum | Cultivar | 1 | Legume | Annual |
Wheat | Triticum aestivum | Cultivar | 1 | Grass | Annual |
Buckwheat | Fagopyrum esculentum | Cultivar | 1 | Forb | Annual |
White mustard | Sinapis alba | Cultivar | 1 | Brassica | Annual |
All cultivar | Cultivar | 4 | Annual | ||
Fallow | N/A | Cultivar | 0 | N/A | N/A |
Silky Lupine | Lupinus sericeus | Native | 1 | Legume | Perennial |
Bluebunch wheatgrass | Pseudoroegneria spicata | Native | 1 | Grass | Perennial |
White yarrow | Achillea millefolium | Native | 1 | Forb | Perennial |
Holboell’s rockcress | Bochera hoellbelii | Native | 1 | Brassica | Perennial |
All native | Native | 4 | Perennial |
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Richards, A.; Estaki, M.; Úrbez-Torres, J.R.; Bowen, P.; Lowery, T.; Hart, M. Cover Crop Diversity as a Tool to Mitigate Vine Decline and Reduce Pathogens in Vineyard Soils. Diversity 2020, 12, 128. https://doi.org/10.3390/d12040128
Richards A, Estaki M, Úrbez-Torres JR, Bowen P, Lowery T, Hart M. Cover Crop Diversity as a Tool to Mitigate Vine Decline and Reduce Pathogens in Vineyard Soils. Diversity. 2020; 12(4):128. https://doi.org/10.3390/d12040128
Chicago/Turabian StyleRichards, Andrew, Mehrbod Estaki, José Ramón Úrbez-Torres, Pat Bowen, Tom Lowery, and Miranda Hart. 2020. "Cover Crop Diversity as a Tool to Mitigate Vine Decline and Reduce Pathogens in Vineyard Soils" Diversity 12, no. 4: 128. https://doi.org/10.3390/d12040128