Research Project: Utilization of the Rhizosphere Microbiome and Host Genetics to Manage Soil-borne Diseases

Location: Physiology and Pathology of Tree Fruits Research

Publications (Clicking on the reprint icon will take you to the publication reprint.)

IGT/LAZY genes are differentially influenced by light and required for light-induced change to organ angle - (Peer Reviewed Journal)

A framework for the targeted recruitment of crop-beneficial soil taxa based on network analysis of metagenomics data - (Peer Reviewed Journal)
Berihu, M., Somera, T.S., Malik, A., Medina, S., Piombo, E., Tal, O., Cohen, M., Ginat, A., Ofek-Lalzar, M., Doron-Faigenboim, A., Mazzola, M., Freilich, S. 2023. A framework for the targeted recruitment of crop-beneficial soil taxa based on network analysis of metagenomics data. Microbiome. 11. Article 8. https://doi.org/10.1186/s40168-022-01438-1.

Direct attenuation of Arabidopsis ERECTA signalling by a pair of U-box E3 ligases - (Peer Reviewed Journal)
Chen, L., Cochran, A.M., Waite, J.M., Shirasu, K., Bemis, S.M., Torii, K.U. 2022. Direct attenuation of Arabidopsis ERECTA signalling by a pair of U-box E3 ligases. Nature Plants. 9:112-127. https://doi.org/10.1038/s41477-022-01303-x.

Transcriptome analysis of transgenic apple fruit overexpressing microRNA172 reveals candidate transcription factors regulating apple fruit development at early stages - (Peer Reviewed Journal)
Zhou, Z., Zhu, Y., Zhang, H., Zhang, R., Gao, Q., Yao, J., Yan, Z. 2021. Transcriptome analysis of transgenic apple fruit overexpressing microRNA172 reveals candidate transcription factors regulating apple fruit development at early stages. PeerJ. 9:e12675. https://doi.org/10.7717/peerj.12675.

The genotype-specific laccase gene expression and lignin deposition patterns in apple root during Pythium ultimum infection - (Peer Reviewed Journal)
Zhu, Y., Zhou, Z. 2021. The genotype-specific laccase gene expression and lignin deposition patterns in apple root during Pythium ultimum infection. Fruit Research. 1. Article 12. https://doi.org/10.48130/FruRes-2021-0012.

Contrasting effects of genotype and root size on the fungal and bacterial communities associated with apple rootstocks - (Peer Reviewed Journal)
Liu, J., Abdelfattah, A., Wasserman, B., Wisniewski, M., Droby, S., Fazio, G., Mazzola, M., Wu, X. 2022. Contrasting effects of genotype and root size on the fungal and bacterial communities associated with apple rootstocks. Horticulture Research. 9. Article uhab013. https://doi.org/10.1093/hr/uhab013.

Laccase directed lignification is one of the major processes associated with the defense response against Pythium ultimum infection in apple roots - (Peer Reviewed Journal)
Zhu, Y., Li, G., Singh, J., Khan, A., Fazio, G., Saltzgiver, M., Xia, R. 2021. Laccase directed lignification is one of the major processes associated with the defense response against Pythium ultimum infection in apple roots. Frontiers in Plant Science. 12. Article 629776. https://doi.org/10.3389/fpls.2021.629776.

Analysis of environmental variables and carbon input on soil microbiome, metabolome and disease control efficacy in strawberry attributable to anaerobic soil disinfestation - (Peer Reviewed Journal)
Hewavitharana, S.S., Klarer, E.R., Muramoto, J., Shennan, C., Mazzola, M. 2021. Analysis of environmental variables and carbon input on soil microbiome, metabolome and disease control efficacy in strawberry attributable to anaerobic soil disinfestation. Microorganisms. 9(8),Article 1638. https://doi.org/10.3390/microorganisms9081638.

Field scale application of Brassica seed meal and anaerobic soil disinfestation for the control of replant disease - (Peer Reviewed Journal)
DuPont, T., Hewavitharana, S., Mazzola, M. 2021. Field scale application of Brassica seed meal and anaerobic soil disinfestation for the control of replant disease. Applied Soil Ecology. 166. Article 104076. https://doi.org/10.1016/j.apsoil.2021.104076.

Comparative analysis of the apple root transcriptome as affected by rootstock genotype and Brassicaceae seed meal soil amendment: Implications for plant health - (Peer Reviewed Journal)
Wang, L., Somera, T.S., Hargarten, H.L., Honaas, L.A., Mazzola, M. 2021. Comparative analysis of the apple root transcriptome as affected by rootstock genotype and Brassicaceae seed meal soil amendment: Implications for plant health. Microorganisms. 9(4). Article 763. https://doi.org/10.3390/microorganisms9040763.

Rotation length, crop rotation, anaerobic soil disinfestation and mustard seed meal affect organic strawberry yield and soil-borne disease incidence in California - (Proceedings)
Zavatta, M., Muramoto, J., Mazzola, M., Shennan, C. 2021. Rotation length, crop rotation, anaerobic soil disinfestation and mustard seed meal affect organic strawberry yield and soil-borne disease incidence in California. Acta Horticulturae. 1309(72):501-508. https://doi.org/10.17660/ActaHortic.2021.1309.72.

MdPR4, a pathogenesis-related protein in apple, is involved in chitin recognition and resistance response to apple replant disease pathogens - (Peer Reviewed Journal)
Zhou, Z., Zhu, Y., Yi, T., Jia-Long, Y., Shuxun, B., Hengtao, Z., Ruiping, Z., Qiming, G., Zhenzhen, L., Zhenli, Y. 2021. MdPR4, a pathogenesis-related protein in apple, is involved in chitin recognition and resistance response to apple replant disease pathogens. Journal of Plant Physiology. 260.Article 153390. https://doi.org/10.1016/j.jplph.2021.153390.

Comprehensive analysis of the apple rhizobiome as influenced by different Brassica seed meals in the same soil/plant system - (Peer Reviewed Journal)
Somera, T.S., Freilich, S., Mazzola, M. 2021. Comprehensive analysis of the apple rhizobiome as influenced by different Brassica seed meals in the same soil/plant system. Applied Soil Ecology. 157. Article 103766. https://doi.org/10.1016/j.apsoil.2020.103766.

Small RNA and degradome sequencing identified microRNA-target gene pairs regulating apple root defense responses towards Pythium ultimum infection - (Abstract Only)
Zhu, Y., Saltzgiver, M.J., Xia, R. 2020. Small RNA and degradome sequencing identified microRNA-target gene pairs regulating apple root defense responses towards Pythium ultimum infection [abstract]. APS Annual Meeting. Plant Health.

Influence of rootstock genotype on efficacy of anaerobic soil disinfestation for control of apple nursery replant disease - (Peer Reviewed Journal)
Hewavitharana, S., Mazzola, M. 2020. Influence of rootstock genotype on efficacy of anaerobic soil disinfestation for control of apple nursery replant disease. European Journal of Plant Pathology. 157:39–57. https://doi.org/10.1007/s10658-020-01977-z.

A systematic analysis of apple root resistance traits to Pythium ultimum infection and the underpinned molecular regulations of defense activation - (Peer Reviewed Journal)
Zhu, Y., Saltzgiver, M.J. 2020. A systematic analysis of apple root resistance traits to Pythium ultimum infection and the underpinned molecular regulations of defense activation. Horticulture Research. 7:1-11. https://doi.org/10.1038/s41438-020-0286-4.

Application sequence modulates microbiome composition, plant growth and apple replant disease control efficiency upon integration of anaerobic soil disinfestation and mustard seed meal amendment - (Peer Reviewed Journal)
Mazzola, M., Graham, D.L., Wang, L., Leisso, R., Hewavitharana, S.S. 2020. Application sequence modulates microbiome composition, plant growth and apple replant disease control efficiency upon integration of anaerobic soil disinfestation and mustard seed meal amendment. Crop Protection. 132. https://doi.org/10.1016/j.cropro.2020.105125.

Use of a summer cover crop as a partial carbon source for anaerobic soil disinfestation in coastal California - (Peer Reviewed Journal)
Muramoto, J., Shennan, C., Mazzola, M., Wood, T., Miethke, E., Resultay, E., Zavatta, M., Koike, S.T. 2020. Use of a summer cover crop as a partial carbon source for anaerobic soil disinfestation in coastal California. Acta Horticulturae. 1270:37-44. https://doi.org/10.17660/ActaHortic.2020.1270.4.

Effects of crop rotation, anaerobic soil disinfestation, and mustard seed meal on disease severity and organic strawberry production in California - (Peer Reviewed Journal)
Shennan, C., Muramoto, J., Baird, G., Zavatta, M., Nobua, B., Mazzola, M. 2020. Effects of crop rotation, anaerobic soil disinfestation, and mustard seed meal on disease severity and organic strawberry production in California. Acta Horticulturae. 1270:63-70. https://doi.org/10.17660/ActaHortic.2020.1270.7.

Transcriptional profiles of MdWRKY33 in apple root in response to infection by Pythium ultimum, abiotic stresses and chemical treatments - (Peer Reviewed Journal)
Zhu, Y., Saltzgiver, M.J. 2019. Transcriptional profiles of MdWRKY33 in apple root in response to infection by Pythium ultimum, abiotic stresses and chemical treatments. International Journal of Plant Pathology. 8(3):87-100. https://doi.org/10.33687/phytopath.008.03.2996.

Temporal dynamics of the soil metabolome and microbiome during simulated anaerobic soil disinfestation - (Peer Reviewed Journal)
Hewavitharana, S., Klarer, E., Reed, A.J., Leisso, R.S., Poirier, B.C., Honaas, L.A., Rudell Jr, D.R., Mazzola, M. 2019. Temporal dynamics of the soil metabolome and microbiome during simulated anaerobic soil disinfestation. Frontiers in Microbiology. 10. https://doi.org/10.3389/fmicb.2019.02365.

Computational approaches for deciphering the functions of microbial communities - (Abstract Only)
Freilich, S., Vetcos, M., Malik, A., Medina, S., Cohen, M., Ofek-Llazar, M., Faiganbion-Doron, A., Mazzola, M. 2019. Computational approaches for deciphering the functions of microbial communities. Symposium Proceedings. p. 22.

Exploring the functional capacity of seed meal-structured microbiomes in the control of apple replant disease - (Abstract Only)
Somera, T.S., Freilich, S., Mazzola, M. 2019. Exploring the functional capacity of seed meal-structured microbiomes in the control of apple replant disease. Symposium Proceedings. p. 44.

Manipulation of the orchard soil microbiome: Implications for soil-borne disease suppression and apple production - (Proceedings)
Mazzola, M., Somera, T.S., Van Horn, C.R., Leisso, R., Freilich, S. 2019. Manipulation of the orchard soil microbiome: Implications for soil-borne disease suppression and apple production. Symposium Proceedings. p. 16.

Apple rootstock genotype influences endophyte and rhizosphere microbial community - (Abstract Only)
Van Horn, C.R., Mazzola, M. 2019. Apple rootstock genotype influences endophyte and rhizosphere microbial community. Phytopathology. 109(11):S3.2.

Exploring the functional capacity of seed meal-structured microbiomes in the control of apple replant disease - (Proceedings)
Somera, T.S., Freilich, S., Mazzola, M. 2019. Exploring the functional capacity of seed meal-structured microbiomes in the control of apple replant disease. Soil Ecology Society Conference. p. 285.

Impacts of anaerobic soil disinfestation carbon source on dynamics of the soil metabolome and microbiome - (Abstract Only)
Klarer, E., Hewavitharana, S., Rudell Jr, D.R., Mazzola, M. 2019. Impacts of anaerobic soil disinfestation carbon source on dynamics of the soil metabolome and microbiome. Phytopathology. 109:S2.69.

Influence of carbon input on anaerobic soil disinfestation efficacy for control of Fusarium wilt in strawberry - (Abstract Only)
Klarer, E., Mazzola, M. 2019. Influence of carbon input on anaerobic soil disinfestation efficacy for control of Fusarium wilt in strawberry. Phytopathology. 109:S2.69.

Multi-site field assessment of bio-renovation methods to control apple replant disease - (Abstract Only)
Hewavitharana, S.S., Dupont, T., Mazzola, M. 2019. Multi-site field assessment of bio-renovation methods to control apple replant disease. Phytopathology. 109:S2.72.

Field evaluation of reduced rate Brassicaceae seed meal amendment and rootstock genotype on the microbiome and control of apple replant disease - (Peer Reviewed Journal)
Wang, L., Mazzola, M. 2019. Field evaluation of reduced rate Brassicaceae seed meal amendment and rootstock genotype on the microbiome and control of apple replant disease. Phytopathology. 109(8):1378-1391. https://doi.org/10.1094/PHYTO-02-19-0045-R.

Evaluating different approaches in the application of phosphonates for the control of apple root diseases - (Peer Reviewed Journal)
Nyoni, M., Lotze, E., Mazzola, M., Wessels, J.B., McLeod, A. 2019. Evaluating different approaches in the application of phosphonates for the control of apple root diseases. Australasian Plant Pathology. 48(5):461-472. https://doi.org/10.1007/s13313-019-00647-x.

Efficacy of fungicide treatments for control of anthracnose canker in young cider apple trees in Western Washington - (Peer Reviewed Journal)
Garton, W., Mazzola, M., Alexander, T.R., Miles, C.A. 2019. Efficacy of fungicide treatments for control of anthracnose canker in young cider apple trees in Western Washington. HortTechnology. 29(1):35-40. https://doi.org/10.21273/HORTTECH04201-18.

The efficacy of semiselective chemicals and chloropicrin/1,3-dichloropropene-containing fumigants in managing apple replant disease in South Africa - (Peer Reviewed Journal)
Nyoni, M., Mazzola, M., Wessels, J.B., McLeod, A. 2019. The efficacy of semiselective chemicals and chloropicrin/1,3-dichloropropene-containing fumigants in managing apple replant disease in South Africa. Plant Disease. 103(6):1363-1373. https://doi.org/10.1094/PDIS-10-18-1844-RE.

Evaluating different approaches for the quantification of oomycete apple replant pathogens, and their relationship with seedling growth reductions - (Peer Reviewed Journal)
Moein, S., Mazzola, M., Spies, C.F., Mcleod, A. 2019. Evaluating different approaches for the quantification of oomycete apple replant pathogens, and their relationship with seedling growth reductions. European Journal of Plant Pathology. 154:243-257.

Identifying an elite panel of apple rootstock germplasm with contrasting root resistance to Pythium ultimum - (Peer Reviewed Journal)
Zhu, Y., Zhao, J., Zhou, Z. 2018. Identifying an elite panel of apple rootstock germplasm with contrasting root resistance to Pythium ultimum. Journal of Plant Pathology & Microbiology. 9(11):1000461. https://doi.org/10.4172/2157-7471.1000461.

Apple nursery trees and irrigation water as potential external inoculum sources of apple replant disease in South Africa - (Peer Reviewed Journal)
Moein, S., Mazzola, M., Ntushelo, N.S., McLeod, A. 2019. Apple nursery trees and irrigation water as potential external inoculum sources of apple replant disease in South Africa. European Journal of Plant Pathology. 153(4):1131-1147. https://doi.org/10.1007/s10658-018-01631-9.

Efficacy of excision, cauterization, and fungicides for management of apple anthracnose canker in maritime climate - (Peer Reviewed Journal)
Garton, W., Mazzola, M., Dasgupta, N., Alexander, T.R., Miles, C.A. 2018. Efficacy of excision, cauterization, and fungicides for management of apple anthracnose canker in maritime climate. HortTechnology. 28(6):728-736. https://doi.org/10.21273/HORTTECH04148-18.

Effect of soil physical conditions on emission of allyl isothiocyanate and subsequent microbial inhibition in response to Brassicaceae seed meal amendment - (Peer Reviewed Journal)
Wang, L., Mazzola, M. 2019. Effect of soil physical conditions on emission of allyl isothiocyanate and subsequent microbial inhibition in response to Brassicaceae seed meal amendment. Plant Disease. 103:846-852. https://doi.org/10.1094/PDIS-08-18-1389-RE.

Timing of perennial canker development in apple trees caused by Neofabraea perennans and Neofabraea kienholzii - (Peer Reviewed Journal)
Aguilar, C., Mazzola, M., Xiao, C. 2019. Timing of perennial canker development in apple trees caused by Neofabraea perennans and Neofabraea kienholzii. Plant Disease. 103(3):555-562. https://doi.org/10.1094/PDIS-06-18-0935-RE.

Interaction of Brassicaceae seed meal soil amendment and apple rootstock genotype on microbiome structure and replant disease suppression - (Peer Reviewed Journal)
Wang, L., Mazzola, M. 2019. Interaction of Brassicaceae seed meal soil amendment and apple rootstock genotype on microbiome structure and replant disease suppression. Phytopathology. 109(4):607-614. https://doi.org/10.1094/PHYTO-07-18-0230-R.

A phenotyping protocol for detailed evaluation of apple root resistance responses utilizing tissue culture micropropagated apple plants - (Peer Reviewed Journal)
Zhu, Y., Saltzgiver, M.J., Zhao, J. 2018. A phenotyping protocol for detailed evaluation of apple root resistance responses utilizing tissue culture micropropagated apple plants. American Journal of Plant Sciences. 9(11):2183-2204. https://doi.org/10.4236/ajps.2018.911158.

Genotype-specific suppression of multiple defense pathways in apple root during infection by Pythium ultimum - (Peer Reviewed Journal)
Zhu, Y., Shao, J.Y., Zhou, Z., Davis, R.E. 2019. Genotype-specific suppression of multiple defense pathways in apple root during infection by Pythium ultimum. Horticulture Research. 6:10. https://doi.org/10.1038/s41438-018-0087-1.

Effects of crop rotation, anaerobic soil disinfestation and mustard seed meal on disease severity and organic strawberry production in California - (Proceedings)
Shennan, C., Muramoto, J., Mazzola, M., Baird, G., Zavatta, M., Nobua, B. 2018. Effects of crop rotation, anaerobic soil disinfestation and mustard seed meal on disease severity and organic strawberry production in California. Symposium Proceedings. p. 11.

Use of a summer cover crop as a partial carbon source for anaerobic soil disinfestation in coastal California - (Proceedings)
Muramoto, J., Shennan, C., Mazzola, M., Wood, T., Resultay, E., Zavatta, M., Koike, S.T. 2018. Use of a summer cover crop as a partial carbon source for anaerobic soil disinfestation in coastal California. Symposium Proceedings. p. 8.

Targeted metabolic profiling indicates apple rootstock genotype-specific differences in primary and secondary metabolite production and validate quantitative contribution from vegetative growth - (Peer Reviewed Journal)
Leisso, R.S., Rudell Jr, D.R., Mazzola, M. 2018. Targeted metabolic profiling indicates apple rootstock genotype-specific differences in primary and secondary metabolite production and validate quantitative contribution from vegetative growth. Frontiers in Plant Science. 9:1336. https://doi.org/10.3389/fpls.2018.01336.

Advances in understanding tree fruit-rhizosphere microbiome relationships for enhanced plant health - (Book / Chapter)
Mazzola, M., Hewavitharana, S.S. 2019. Advances in understanding tree fruit-rhizosphere microbiome relationships for enhanced plant health. In: Lang, G., editor. Achieving Sustainable Cultivation of Temperate Zone Free Fruits and Berries. Volume 1: Physiology, Genetics and Cultivation. Cambridge, UK: Burleigh Dodds Science, p. 3-30. https://doi.org/10.19103/AS.2018.0040.01.

Development and application of biologically-based methods to control soil-borne diseases - (Proceedings)
Mazzola, M., Wang, L., Hewavitharana, S. 2018. Development and application of biologically-based methods to control soil-borne diseases. Symposium Proceedings. p. 106.1-106.2.

Temporal dynamics of the soil metabolome and microbiome in response to anaerobic soil disinfestation - (Abstract Only)
Hewavitharana, S.S., Leisso, R.S., Honaas, L.A., Rudell Jr, D.R., Mazzola, M. 2018. Temporal dynamics of the soil metabolome and microbiome in response to anaerobic soil disinfestation. Phytopathology. 108(10):S1.101.

Integrating host resistance and organic amendments in a chemical-independent approach to managing macrophomina crown rot in strawberries - (Abstract Only)
Winslow, J., Mazzola, M., Holmes, G.J., Ivors, K. 2018. Integrating host resistance and organic amendments in a chemical-independent approach to managing macrophomina crown rot in strawberries. Phytopathology. 108(10):S1-175.

Anaerobic disinfestation induced changes to the soil microbiome, disease incidence and strawberry fruit yields in California field trials - (Peer Reviewed Journal)
Mazzola, M., Muramoto, J., Shennan, C. 2018. Anaerobic disinfestation induced changes to the soil microbiome, disease incidence and strawberry fruit yields in California field trials. Applied Soil Ecology. 127:74-86. https://doi.org/10.1016/j.apsoil.2018.03.009.

Potato scab management with Brassica biofumigation and effect of volatiles on Streptomyces growth - (Abstract Only)
Gouws-Meyer, R., Mcleod, A., Mazzola, M. 2020. Potato scab management with Brassica biofumigation and effect of volatiles on Streptomyces growth. Acta Horticulturae. https://doi.org/10.17660/ActaHortic.2020.1269.4.

Involvement of Dactylonectria and Ilyonectria spp. in tree decline affecting multigeneration apple orchards - (Peer Reviewed Journal)
Manici, L.M., Caputo, F., Sacca, M.L., Kelderer, M., Nicoletti, F., Topp, A.R., Mazzola, M. 2018. Involvement of Dactylonectria and Ilyonectria spp. in tree decline affecting multigeneration apple orchards. Plant and Soil. https://doi.org/10.1007/s11104-018-3571-3.

Mobilizing the rhizosphere microbiome to enhance orchard system resilience - (Abstract Only)
Mazzola, M. 2018. Mobilizing the rhizosphere microbiome to enhance orchard system resilience. Meeting Proceedings. Available: https://conference.ufz.de/frontend/index.php?page_id=3249&v=List&do=15&day=1447&ses=912#.

Control of bull’s-eye rot of apple caused by Neofabraea perennans and Neofabraea kienholzii using pre- and postharvest fungicides - (Peer Reviewed Journal)
Aguilar, C.G., Mazzola, M., Xiao, C. 2018. Control of bull’s-eye rot of apple caused by Neofabraea perennans and Neofabraea kienholzii using pre- and postharvest fungicides. Plant Disease. 102(5):905-910. https://doi.org/10.1094/PDIS-09-17-1363-RE.

A review of apple anthracnose canker biology and management in cider apple orchards in the Maritime Pacific Northwest - (Peer Reviewed Journal)
Garton, W.J., Devetter, L.W., Mazzola, M., Miles, C.A. 2018. A review of apple anthracnose canker biology and management in cider apple orchards in the Maritime Pacific Northwest. Journal of American Pomological Society. 72(2):113-121.

Refining ASD for disease management in strawberry and apple production - (Proceedings)
Mazzola, M., Hewavitharana, S.S., Muramoto, J., Shennan, C. 2017. Refining ASD for disease management in strawberry and apple production. International Conference on Methyl Bromide Alternatives and Emissions Reductions. p. 4.1-4.2.

Anaerobic soil disinfestation for controlling Fusarium wilt in strawberies - (Proceedings)
Muramoto, J., Shennan, C., Zavatta, M., Mazzola, M., Ivors, K. 2017. Anaerobic soil disinfestation for controlling Fusarium wilt in strawberies. International Conference on Methyl Bromide Alternatives and Emissions Reductions. p. 31.1-31.4.

Using RNA-Seq data to select refence genes for normalizing gene expression in apple roots - (Peer Reviewed Journal)
Zhou, Z., Cong, P., Tian, Y., Zhu, Y. 2017. Using RNA-Seq data to select refence genes for normalizing gene expression in apple roots. PLoS One. https://doi.org/10.1371/journal.pone.0185288.

Management of bull’s eye rot using preharvest and postharvest fungicides - (Abstract Only)
Sikdar, P., Mazzola, M. 2017. Management of bull’s eye rot using preharvest and postharvest fungicides. Phytopathology. 107(Suppl.5), 192.