Laboratory of Beneficial Microbes (Probiotics) for Crops and Sustainable Agriculture Kits (SAKs) for Subsistence Farmers
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Publications
​Books (Journal Publications Below)

Farmpedia: The Encyclopedia for Small Scale Farmers (Edition 3, 2024) (Farmpedia.org) (MN Raizada, Editor) 
This ebook consists of 226 chapters that critically analyze appropriate agro-ecological technologies for subsistence farmers (including beneficial microbial inoculants) with practical tips to help get started, with language that is easy to understand. It is intended for NGOs, charitable groups, agricultural extension officers, farmers and scientists. Two new chapters are added monthly. Farmpedia began in 2022 (Edition 1) with help from Associate Editor Jen Wilker (now at CIAT, Colombia). The Publisher is Phelystus Kubwa (Nairobi, Kenya).  Farmpedia is open access, free and available online at www.Farmpedia.org

A Picture Book of Best Practices for Subsistence Farmers (2017). By MN Raizada with illustrations by L. Jay Smith (190 pages, 5 versions)
This book consists of 145 best practices (both scientific and indigenous) presented in a graphical format to assist illiterate farmers. It features beautiful illustrations from talented computer graphics artist, L. Jay Smith. The book is open access, copyright-free and available online at SAKbooks.com. Organizations that work with farmers can download compilations of individual lessons to create customized booklets and add their own text translations. Furthermore, 5 ethnic versions of the book have been created, representing the major tropical/subtropical regions of the world. 
Related: A Picture Booklet of Best Practices for Nepalese Farmers (2016). 
sak_picture_booklet_nepali_final_aug8_2016.pdf
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Journal Articles and Book Chapters 

These PDFs are meant for personal use only. By downloading one of these PDFs, you are agreeing not to distribute to a third party. Hint: PDFs download much faster if you click on the PDF icon directly. Many of the Lab's papers can also be easily accessed via Loop.

111. Thilakarathna, M.S., Watts, S., Thompson, M.E.H., Goron, T., Chu, G., Szczyglowski, K., Morrison, M.J. and Raizada, M.N. (2025) Effective rhizobia relieves negative effects of drought stress during the vegetative stage in soybean under field conditions. Journal of Agronomy and Crop Science (In press)

110. Pudasaini R., Amyotte J., Brettingham DJL and Raizada, MN (2025) Physiological, metabolomic, morphological and root system architecture acclimation responses to drought in the African orphan millet, White Fonio (Digitaria exilis). Plant and Soil  (published January 7, 2025) 
​
https://doi.org/10.1007/s11104-024-07159-8
FULL TEXT VIEW
https://rdcu.be/d5xWP

109. Pudasaini R. and Raizada, MN (2025) Potential of short-duration millets as a post-winter wheat crop in Ontario, Canada. Agronomy Journal, e21740 
http://dx.doi.org/10.1002/agj2.21740
​​OPEN ACCESS

108. Thompson, MEH, Shrestha, A., Khalaf, E.M., Rinne, J., Limay-Rios, V., Reid, L.M. and Raizada MN (2024) Analysis of the cultured microbiome of fertilization-stage silks (styles) reveals taxonomic relationships across North American maize genotypes and heterotic groups. Bacteria 3, 476-498.
https://www.mdpi.com/2674-1334/3/4/32
OPEN ACCESS​

107. Thompson, M.E.H. and Raizada, M.N. (2024) Biologically relevant methods to test how microbes colonize maize styles (silks): Case study of a Pantoea strain. Bacteria 3, 287-298. 
https://www.mdpi.com/2674-1334/3/4/19 
​
OPEN ACCESS

106. Pudasaini, R. and Raizada, M.N. (2024) Nodule crushing: a novel technique to decentralize rhizobia inoculant technology and empower small-scale farmers to enhance legume production and income. Frontiers in Sustainable Food Systems  8, 1423997.
https://www.frontiersin.org/journals/sustainable-food-systems/articles/10.3389/fsufs.2024.1423997/full​
OPEN ACCESS

105. Thompson, M.E.H. and Raizada, M.N. (2024) Protocols to enable fluorescence microscopy of microbial interactions on living maize silks (style tissue). Journal of Microbiological Methods 10, 1016
​
https://doi.org/10.1016/j.mimet.2024.107027
​OPEN ACCESS

104. Thompson, M.E.H. and Raizada, M.N. (2024) The Microbiome of Fertilization-Stage Maize Silks (Style) Encodes Genes and Expresses Traits that Potentially Promote Survival in Pollen/Style Niches and Host Reproduction. Microorganisms 12, 1473. 
https://doi.org/10.3390/microorganisms12071473
OPEN ACCESS

103. Shrestha, A., Limay-Rios, V., Brettingham, D.J.L. and Raizada M.N. (2024) Maize pollen carry bacteria that suppress a fungal pathogen that enters through the male gamete fertilization route. Frontiers in Plant Science 14, 1286199.
https://www.frontiersin.org/articles/10.3389/fpls.2023.1286199/abstract​
OPEN ACCESS

102. Khalaf, E.M.*, Shrestha, A.*, Reid, M., McFadyen, B.J. and Raizada M.N. (2023) Conservation and diversity of the pollen microbiome of pan-American maize using PacBio and MiSeq. Frontiers in Microbiology 14, 1276241.
​(*co-equal first authors)
https://www.frontiersin.org/articles/10.3389/fmicb.2023.1276241/abstract​
OPEN ACCESS

101. Shrestha, A., Limay-Rios, V., Brettingham, D.J.L. and Raizada MN (2023) Bacteria existing in pre-pollinated styles (silks) can defend the exposed male fertilization channel of maize against an environmental Fusarium pathogen. Frontiers in Plant Science 14, 1292109
https://www.frontiersin.org/articles/10.3389/fpls.2023.1292109/full​
OPEN ACCESS

100. Thompson, MEH, Shrestha, A., Rinne, J., Limay-Rios, V., Reid, L. and Raizada MN (2023) The cultured microbiome of pollinated maize silks shifts after infection with Fusarium graminearum and varies by distance from the site of pathogen inoculation. Pathogens 12, 1322 [featured on journal website main page]
https://doi.org/10.3390/pathogens12111322
OPEN ACCESS

99. Pudasaini R., Hewedy O, and Raizada MN (2023) Improving field legume nodulation by crushing nodules onto seeds: implications for small-scale farmers. Frontiers in Agronomy 5, 1161978
https://www.frontiersin.org/articles/10.3389/fagro.2023.1161978/full
OPEN ACCESS

98. Khadka K, Kaviani M, Raizada MN and Navabi A (2021) Phenotyping and identification of reduced height (Rht) alleles (Rht-B1b and Rht-D1b) in a Nepali spring wheat (Triticum aestivum L.) diversity panel to enable seedling vigor selection. Agronomy 11, 2412
www.mdpi.com/2073-4395/11/12/2412
OPEN ACCESS
98._khadka_2021_agronomy_rht_coleoptiles.pdf
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97. Dumigan CR, Muileboom J, Gregory J, Shrestha A, Hewedy OA and Raizada MN (2021) Ancient relatives of modern maize from the center of maize domestication and diversification host endophytic bacteria that confer tolerance to nitrogen starvation. Frontiers in Plant Science 12: 660673
OPEN ACCESS
https://www.frontiersin.org/articles/10.3389/fpls.2021.660673/full
97._dumigan_frontiers_2021_ancient_nue_microbes.pdf
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96. Thilakarathna MS, Torkamaneh D, Bruce RW, Rajcan I, Chu G, Grainger CM, Szczyglowski, Hill B and Raizada MN (2021) Testing whether pre-pod-fill symbiotic nitrogen fixation in soybean is subject to drift or selection over 100 years of soybean breeding. Frontiers in Agronomy 3: 725813.
OPEN ACCESS
https://www.frontiersin.org/articles/10.3389/fagro.2021.725813/full
96._thilakarathna_2021_frontiers_soybean_snf_variation.pdf
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95. Khalaf EM, Shresha A, Rinne J, Lynch MDJ, Shearer CR, Limay-Rios V, Reid LM and Raizada MN (2021) Transmitting silks of maize have a complex and dynamic microbiome. Scientific Reports 11: 13215
https://www.nature.com/articles/s41598-021-92648-4
OPEN ACCESS
95._khalaf_et_al-2021-scientific_reports.pdf
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95._khalaf_supplementary.pdf
File Size: 4121 kb
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95._khalaf_supplementary_dataset.xlsx
File Size: 209 kb
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94. Khadka K, Burt AJ, Earl HJ, Raizada MN and Navabi A (2021) Does leaf waxiness confound the use of NDVI in the assessment of chlorophyll when evaluating genetic diversity panels of wheat? Agronomy 11, 486
www.mdpi.com/2073-4395/11/3/486
OPEN ACCESS

93. Sousa EC and Raizada MN (2020) Contributions of African crops to American culture and beyond: The Slave Trade and other journeys of resilient peoples and crops. Frontiers in Sustainable Food Systems 4: 586340
https://www.frontiersin.org/articles/10.3389/fsufs.2020.586340/abstract 

Viewed >40,000 times since publication.
OPEN ACCESS

92. Devkota R , Hambly Odame H, Fitzsimons J, Pudasaini R, and Raizada MN (2020) Evaluating the Effectiveness of Picture-Based Agricultural Extension Lessons Developed Using Participatory Testing and Editing with Smallholder Women Farmers in Nepal. Sustainability 12, 9699
https://www.mdpi.com/2071-1050/12/22/9699  
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92._devkota_2020_sustainability_sak_picture_book.pdf
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91. Khadka K, Torkamaneh D, Kaviani M, Belzile F, Raizada MN and Navabi A (2020) 
Population structure of Nepali spring wheat (Triticum aestivum L​.) germplasm. BMC Plant Biology 20:530

https://link.springer.com/article/10.1186/s12870-020-02722-8
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91._khadka_2020_bmc_plant_biology_pop_structure_nepali_wheat.pdf
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90. Khalaf EM and Raizada MN. 2020. Draft genome sequences of six strains of Lactococcus lactis (phylum Firmicutes), spanning the seeds of Cucumis sativus L. (cucumber), Cucumis melo L. (cantaloupe), and Cucurbita pepo var.turbinate (acorn squash). Microbiol Resour Announc 9:e00665-20.
https://doi.org/10.1128/MRA.00665-20.

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90._khalaf_and_raizada_2020_9_37_lactococcus_lactis_from_cucurbit_seeds.pdf
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89. Khalaf EM and Raizada MN. 2020. Draft genome sequences of Pantoea agglomerans, Paenibacillus polymyxa, and Pseudomonas sp.strains, seed biogel-associated endophytes of Cucumis sativus L. (cucumber) and Cucumis
melo L. (cantaloupe). Microbiol Resour Announc 9:e00667-20.
https://doi.org/10.1128/MRA.00667-20.
OPEN ACCESS
89._khalaf_and_raizada_2020_9_32_mra_cucumber_and_cantaloupe_biogel.pdf
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88. Khadka K, Raizada MN and Navabi A (2020)  Recent Progress in Germplasm Evaluation and Gene Mapping to Enable Breeding of Drought-Tolerant Wheat. Frontiers in Plant Science 11:1149
https://www.frontiersin.org/articles/10.3389/fpls.2020.01149/full
OPEN ACCESS
88._khadka_2020_frontiers_wheat_germplasm_evaluation_drought.pdf
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87. Khalaf EM and Raizada MN. 2020. Draft genome sequences of Bacillus and Paenibacillus species isolated from seeds of Citrullus lanata (watermelon), Cucurbita moschata (butternut squash), and Cucurbita pepo L. var. pepo L. (pumpkin). Microbiol Resour Announc 9:e00727-20. https://doi.org/10.1128/MRA.00727-20.
OPEN ACCESS
87._khalaf_and_raizada_2020_9_34_bacillus_and_paenibacillus_from_melon_squash_pumpkin.pdf
File Size: 164 kb
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86. Khalaf EM and Raizada MN. 2020. Draft genome sequences of seven strains of Paenibacillus spp. (phylum Firmicutes) inhabiting the seeds of Cucumis melo L. (cantaloupe) and exhibiting plant probiotic traits. Microbiol Resour Announc 9:e00715-20. 
​
https://doi.org/10.1128/MRA.00715-20.
OPEN ACCESS
86._khalaf_and_raizada_2020_mra_9_34_aenibacillus_from_cantaloupe_seeds.pdf
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85. Khadka K, Earl HJ, Raizada MN and Navabi A (2020) A Physio-Morphological Trait-Based Approach for Breeding Drought Tolerant Wheat. Frontiers in Plant Science 11: 715
https://www.frontiersin.org/articles/10.3389/fpls.2020.00715/full

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85._khadka_2020_frontiers_physiol_drought_review.pdf
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84. Devkota R, Pant LP, Gartaula HN, Patel K, Gauchan D, Hambly-Odame H, Thapa B, and Raizada MN (2020)  Responsible Agricultural Mechanization Innovation for the Sustainable Development of Nepal’s Hillside Farming System. Sustainability 12, 374 [Selected as Editor's Choice]
https://www.mdpi.com/2071-1050/12/1/374
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84._devkota_et_al_2020_small_scale_mechanization_nepal_sustainability.pdf
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83. Chapagain T, Lee EA and Raizada MN (2020)  The potential of multi-species mixtures to diversify cover crop benefits. Sustainability 12, 2058.
https://www.mdpi.com/2071-1050/12/5/2058 
​www.mdpi.com/2071-1050/12/5/2058

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83._chapagain_2020_cover_crop_multimixes.pdf
File Size: 1717 kb
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82. Khalaf EM and Raizada MN. 2020. Draft genome sequences of Acinetobacter sp. strain EKM10A, Enterobacter hormaechei EKM10E, and Enterobacter hormaechei EKM11E (phylum Proteobacteria) colonizing the seed surface biogel of Echinocystis lobata (wild cucumber). Microbiol Resour Announc 9:e00184 20. 
https://doi.org/10.1128/MRA.00184-20

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82._khalaf_and_raizada_2020_mra_9_20_ekm10a_ekm10e_ekm11e_seed_biogel.pdf
File Size: 158 kb
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81. Khalaf EM and Raizada MN. 2020. Draft genome sequence of Bacillus sp. strain EKM601B (phylum Firmicutes), living inside the seeds of Luffa acutangula (Chinese okra). Microbiol Resour Announc 9:e00180-20.
https://doi.org/10.1128/MRA.00180-20.

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81._khalaf_and_raizada_2020_9_20_mra_ekm601b_luffa_seeds.pdf
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80. Soliman SSM and Raizada MN (2020)  Sites of biosynthesis and storage of Taxol in Taxus media (Rehder) plants: Mechanism of accumulation. Phytochemistry 175:112369  (Selected to be on the Cover)
www.sciencedirect.com/science/article/abs/pii/S0031942220300224
80._soliman_and_raizada_2020_phytochemistry_with_cover_page.pdf
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79. Johnston-Monje, D, Castillo-Avila, DK, Raizada, MN, Becerra Lopez-Lavalle, L.A. (2019) Paying the Rent: How Endophytic Microorganisms Help Plant Hosts Obtain Nutrients. In Comprehensive Biotechnology, Vol. 4, Moo-Young, M., Ed., Elsevier: Pergamon, pp 770–788. 
79._johnston_monje_2019_endophyte_book_chapter_paying_rent.pdf
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78. Thilakarathna MS and Raizada MN (2019)  A biosensor-based assay (GlnLux-agar) shows defoliation triggers rapid release of glutamine from nodules and young roots of forage legumes. Phytobiomes 3:85-91
https://apsjournals.apsnet.org/doi/full/10.1094/PBIOMES-03-19-0014-R​ 
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78._thilakarthna_2019_phytobiomes_glnlux_defoliation.pdf
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77. Chapagain, T., B. Ghimire, R. Pudasaini, K. Gurung, K. Choi, L. Rai, S. Magar, B. BK. and M. N. Raizada (2019) The underutilized terrace wall can be intensified to improve farmer livelihoods. Agronomy for Sustainable Development 39:29
https://link.springer.com/article/10.1007/s13593-019-0574-2
77._chapagain2019_article_theunderutilizedterracewallcan.pdf
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76. Thilakarathna MS, Chapagain T, Ghimire B, Pudasaini R, Tamang BB, Gurung K, Choi K, Rai L, Magar S, Bishnu BK, Gaire S, Raizada MN (2019) Evaluating the effectiveness of rhizobium inoculants and micronutrients as technologies for Nepalese common bean smallholder farmers in the real-world context of highly variable hillside environments and indigenous farming practices. Agriculture 9: 20
https://www.mdpi.com/2077-0472/9/1/20/htm​
​OPEN ACCESS
76._thilakarathna_raizada_2019_agriculture_nepal_rhizobia.pdf
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75. Thompson MEH and Raizada MN (2018) Fungal Pathogens of Maize Gaining Free Passage Along the Silk Road. Pathogens 7:81 (Selected as Editor's Choice)
https://www.mdpi.com/2076-0817/7/4/81
OPEN ACCESS
75._thompson_and_raizada_2018_silk_pathogens_review.pdf
File Size: 804 kb
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74. Dumigan CR, Perry GE, Pauls KP, and Raizada MN (2018) Draft genome sequence of Enterobacter cloacae 3D9 (Phylum Proteobacteria). Microbiology Resource Announcements (In press, DOI: 10.1128/MRA.00902-18)
https://mra.asm.org/content/7/16/e00902-18
OPEN ACCESS
74._dumigan_raizada_2018_mra_3d9_genome_sequence.pdf
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73. Thilakarathna MS and Raizada MN (2018) Visualizing glutamine accumulation in root systems involved in the legume-rhizobia symbiosis by placement on agar embedded with companion biosensor cells. Phytobiomes (https://doi.org/10.1094/PBIOMES-07-18-0031-TA)

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Selected as Editor's pick
73._thilakarathna_raizada_2018_phytobiomes_glnlux_imaging.pdf
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72. Chapagain T, Ghirmire B, Pudasaini R, Gurung K, Choi K, Rai L, Magar S, Bishnu BK and Raizada MN (2018)  Intercropping of maize, millet, mustard, wheat and ginger increased land productivity and potential economic returns for smallholder terrace farmers in Nepal. Field Crops Research 227: 91-101
72._chapagain_2018_field_crop_research_nepal_intercropping.pdf
File Size: 1892 kb
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71. Dumigan CR, Perry GE, Pauls KP, and Raizada MN. 2018. Draft genome sequence of Enterobacter cloacae 3F11 (phylum Proteobacteria). Microbiology Resource Announcements 7:e00846-18. 
https://doi.org/10.1128/MRA.00846-18

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71._dumigan_2018_micro_res_announce_3f11_zeanic_p-solubilizing.pdf
File Size: 111 kb
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70. Thilakarathna MS and Raizada MN (2018) Challenges in Using Precision Agriculture to Optimize Symbiotic Nitrogen Fixation in Legumes: Progress, Limitations and Future Improvements Needed in Diagnostic Testing. Agronomy 8(5):78
http://www.mdpi.com/2073-4395/8/5/78
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70._thilakarathna_2018_agronomy_precision_agriculture_snf.pdf
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69. Soliman SSM and Raizada MN (2018) Darkness: A crucial factor in fungal Taxol production. Frontiers in Microbiology 9: 353
https://www.frontiersin.org/articles/10.3389/fmicb.2018.00353/full
​
OPEN ACCESS
69._soliman_raizada_2017_frontiers_taxol_light.pdf
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68. Khalaf EM and Raizada MN (2018) Bacterial seed endophytes of domesticated cucurbits antagonize fungal and oomycete pathogens including powdery mildew. Frontiers in Microbiology (Feb 5, 2018)
​
https://doi.org/10.3389/fmicb.2018.00042
​
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68._khalaf_and_raizada_2018.pdf
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67. Nameth MB, Goron TL, Dinka SJ, Morris A, English J, Lewis D, Oro R, and Raizada MN (2018) The initial hours of post-excision light are critical for adventitious root regeneration from Arabidopsis thaliana (L.) Heynh. cotyledon explants. In Vitro Cellular & Developmental Biology - Plant  54(3): 273-290
https://link.springer.com/article/10.1007/s11627-017-9880-z
67._nameth_2018_in_vitro_light_root_regeneration.pdf
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Selected as a Journal Highlight in the In Vitro Report, an official publication of the Society for In Vitro Biology ​

66. Raizada MN (2017) Challenges and Solutions for Subsistence Farmers. In Plants, Genes and Agriculture: Sustainability through Biotechnology (Maarten J. Chrispeels and Paul Gepts, Editors). Sinauer Assoc. Inc. and Oxford University Press.
New undergraduate university textbook
Amazon link

65. Shehata HR, Dumigan C, Watts S and Raizada MN (2017) An endophytic microbe from an unusual volcanic swamp corn seeks and inhabits root hair cells to extract rock phosphate. Scientific Reports  7:13479
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65._shehata_et_al-2017-scientific_reports_published_pdf_copy.pdf
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Selected as one of the top25 most accessed articles in Plant Science in this journal in 2017 (within the Top 100 List).

64. Shehata HR, Lyons EM and Raizada MN (2017) Turfgrasses as model assay systems for high-throughput in planta screening of beneficial endophytes isolated from cereal crops. Symbiosis (DOI: 10.1007/s13199-017-0511-6)
64._shehata_2017_symbiosis_turf_model_system.pdf
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63. Thilakarathna MS, Moroz N and Raizada MN (2017) A biosensor-based leaf punch assay for glutamine correlates to symbiotic nitrogen fixation measurements in legumes to permit rapid screening of rhizobia inoculants under controlled conditions. Frontiers in Plant Science  8: 1714
OPEN ACCESS
​​This study uses our microbial biosensor-based GlnLux precision agriculture invention.
63._thilakarathna_and_raizada_2017_frontiers_glnlux_leaf_assay.pdf
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62. Goron TL and Raizada MN (2017) Biosensor-mediated in situ imaging defines the availability period of assimilatory glutamine in maize seedling leaves following nitrogen fertilization. Nitrogen 1:2
​
​​OPEN ACCESS
​
This study uses our microbial biosensor-based GlnLux precision agriculture invention.
62._goron_et_al_2017_nitrogen_pulse_chase_.pdf
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61. Shehata HR and Raizada MN (2017) A Burkholderia endophyte of the ancient maize landrace Chapalote utilizes c-di-GMP-dependent and –independent signaling to suppress diverse plant fungal pathogen targets. FEMS Microbiology Letters 364: fnx138

60. Goron TL, Nederend J, Stewart G, Deen B, and Raizada MN (2017) ​Mid-season leaf glutamine predicts end-season maize grain yield and nitrogen content in response to nitrogen fertilization under field conditions. Agronomy 7(2):41
​
​​OPEN ACCESS
This study uses our microbial biosensor-based GlnLux precision agriculture invention.
60._goron_raizada_agronomy_glnlux_field.pdf
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 59. Chapagain T and Raizada MN (2017) Impacts of natural disasters on smallholder farmers: Gaps and recommendations. Agriculture and Food Security 6:39
​
​​OPEN ACCESS
​      This paper introduces the concept of low cost, emergency Sustainable Agriculture Kits (eSAKs) to help farmers after a disaster.
      Featured in a news release by the University of Guelph:

https://news.uoguelph.ca/2017/05/profs-innovation-aids-natural-disaster-recovery/
​
  Viewed nearly 50,000 times since publication.
59._chapagain_raizada_2017_agric_food_security_esak_disaster.pdf
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58. Chapagain T and Raizada MN (2017) Agronomic challenges and opportunities for smallholder terrace agriculture in developing countries. Frontiers in Plant Science 8: 331 (provisional PDF online. doi: 10.3389/fpls.2017.00331)
​
​​OPEN ACCESS
 Viewed 43,000 times since publication.
58._chapagain_and_raizada_2017_frontiers_in_plant_science_terrace_farming_review.pdf
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57. Small FAA and Raizada MN (2017) Mitigating dry season food insecurity in the subtropics by prospecting drought-tolerant, nitrogen-fixing weeds. Agriculture & Food Security 6:23
​​​OPEN ACCESS
small_et_al-2017-agriculture___food_security.pdf
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56. Raizada MN, Goron TL, Bannerjee O, Quach Mason M, Pautler M, Brazolot J, Morris A, Kajenthira A, Dinka S, DiMeo N (2017) Loss of developmental pluripotency occurs in two stages during leaf aging in Arabidopsis thaliana. In Vitro Cellular & Developmental Biology - Plant 53: 178-187
56._raizada_2017_in_vitro_age_pluripotency.pdf
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55. Shehata HR, Griffiths MW and Raizada MN (2017) Seeds of the wild progenitor of maize possess bacteria that antagonize foodborne pathogens. Foodborne Pathogens and Disease 14: 4  (ePub Feb 10, 2017 doi:10.1089/fpd.2016.2225)
55._shehata_food_pathogens_disease_2017.pdf
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54. Thilakarathna MS and Raizada MN (2017) A meta-analysis of the effectiveness of diverse rhizobia inoculants on soybean traits under field conditions. Soil Biology and Biochemistry  105: 177-196
54._thilakarathna_and_raizada_2017_-_soybean_inoculant_review.pdf
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53. Quach Mason, M, Goron TL, Dziewiecka Arnold E, Dickinson P, Kajenthira A, Dinka SJ, Oro R, and Raizada MN (2017) Pyramid screening: combining three genetic screens into one efficient screen for shoot regeneration mutants in Arabidopsis thaliana. Journal of Plant Growth Regulation (Online Jan 21, 2017 doi:10.1007/s00344-016-9651-9)
53._quach_2017_j_plant_growth_regulation_pyramid_screening.pdf
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52. Goron TL and Raizada MN (2016) Biosensor-based spatial and developmental mapping of maize leaf glutamine at vein-level resolution in response to different nitrogen rates and uptake/assimilation durations. BMC Plant Biology 16:230
​​OPEN ACCESS
​
This study uses our microbial biosensor-based GlnLux precision agriculture invention.
53._goron_raizada_2016_bmc_plant_biology_glnlux_maize_vein_resolution.pdf
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51. Thilakarathna MS, McElroy M, Chapagain T, Papadopoulos YA and Raizada MN (2016) Belowground nitrogen transfer from legumes to non-legumes under managed herbaceous cropping systems. A review. Agronomy for Sustainable Development 36:58
52._thilakarathna_2016_agron_sustain_dev_n_transfer.pdf
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50. Shehata HR​, Ettinger CL, Eisen JA and Raizada MN (2016) Genes required for the anti-fungal activity of a bacterial endophyte isolated from a corn landrace grown continuously by subsistence farmers since 1000 BC. Frontiers in Microbiology 7: 1548
​
OPEN ACCESS
shehata_2016_frontiers_in_microbiology_chapalote_endophyte_1000bc.pdf
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49. Mousa WK, Shearer C, Limay-Rios V, Ettinger CL, Eisen JA, Raizada MN (2016) Root hair-endophyte stacking (RHESt) in finger millet creates a physico-chemical barrier to trap the fungal pathogen Fusarium graminearum. Nature Microbiology  1: 16167 (Article)
​
​
A preprint of this paper is available for free at http://biorxiv.org/content/early/2016/08/25/071548
​
Cool finger millet root video taken by Walaa Mousa of the phenomenon: The root is the vertical purple-red column on the right. Here Fusarium fungal pathogen was added at a distance at the upper left (not visible), and in response, seed-coated endophytic bacteria M6 (GFP-labelled, green) has swarmed towards it, apparently exited, and multiplied dramatically on the left surface of the root (rhizoplane). In parallel, M6 has apparently induced dramatic growth of root hairs (long purple strands on the left, bending vertically and forming a thick mat) onto which the endophyte cells are starting to stack as green layers, similar to a lasagna (in the analogy, the root hairs are the red noodle sheets, and the filling is the endophytic bacteria in green). As a result, multiple barriers are formed against the Fusarium pathogen. Within this complex, M6 produces potent fungicides to kill invading Fusarium so that it cannot enter into the root.

The significance of this discovery is explained in our Press Coverage:


​Press coverage - Radio interview - Canadian Broadcasting Corporation (CBC) "Quirks and Quarks" 
Press coverage  - UofG Press Release
Press coverage - Science Daily
Press coverage - Nature Middle East
49._mousa_raizada_2016_nature_microbiology_small.pdf
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49._mousa_raizada_2016_supplementary_info_nature_microbiology_small.pdf
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48. Mousa WK, Schwan A and Raizada MN (2016) Characterization of antifungal natural products isolated from endophytic fungi of finger millet (Eleusine coracana). Molecules 21: 1171
​OPEN ACCESS
48._mousa_2016_molecules_antifungal_natural_products.pdf
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47. Khalaf EM and Raizada MN (2016) Taxonomic and functional diversity of cultured seed associated microbes of the cucurbit family. BMC Microbiology 16: 131
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47._khalaf_and_raizada_2016_bmc_microbiology_cucurbit_seed_endophytes.pdf
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46. Johnston-Monje D,  Lundberg DS, Lazarovits G, Reis VM and Raizada MN (2016) Bacterial populations in juvenile maize rhizospheres originate from both seed and soil. Plant and Soil 405: 337
​
OPEN ACCESS
46._jonston_monje_2016_plant_soil_soil_and_seed_originating_endophytes_maize.pdf
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45. Mousa, W.K. and Raizada, M.N. (2016) Natural Disease Control in Cereal Grains. In Encyclopedia of Food Grains. 2nd Edition. pp. 257-263. (Eds: C. Wrigley, H. Corke, K. Seetharaman, J. Faubion ). Oxford: Academic Press.
45._mousa_2016_grain_disease_book_chapter.pdf
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44. Shehata HR, Lyons EM, Jordan KS and Raizada MN (2016) Bacterial endophytes from wild and ancient maize are able to suppress the fungal pathogen Sclerotinia homoeocarpa. Journal of Applied Microbiology  120: 756-769
shehata_2016_jam_anti_dollar_spot_endophytes.pdf
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43. Shehata HR, Lyons EM, Jordan KS and Raizada MN (2016) Relevance of in vitro agar based screens to characterize the anti-fungal activities of bacterial endophyte communities. BMC Microbiology 16:8
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shehata_2016_bmc_microbiology_in_vitro_vs_in_planta_screens.pdf
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42. Mousa WK, Schwan A, Davidson J, Strange P, Liu H, Zhou T, Auzanneau F-I and Raizada MN (2015) An endophytic fungus isolated from finger millet (Eleusine coracana) produces anti-fungal natural products. Frontiers in Microbiology 6, 1157
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43._mousa_2015_frontiers_maize_fungal_endophyte_wf4_against_fusarium.pdf
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41. Mousa WK, Shearer C, Limay-Rios V, Zhou T and Raizada MN (2015) Bacterial endophytes from wild maize suppress Fusarium graminearum in modern maize and inhibit mycotoxin accumulation. Frontiers in Plant Science 6, 805.
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42._mousa_et_al_frontiers_in_plant_sci__2015__maize_endophytes_against_fusarium.pdf
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40. Soliman SM, Greenwood JS, Bombarely A, Mueller LA, Tsao R, Mosser DD and Raizada MN (2015) An endophyte constructs fungicide-containing extracellular barriers for its host plant. Current Biology 25, 1-7
​
OPEN ACCESS
-This paper, later selected as the Editor's Choice Discovery in Plant Biology by The Scientist magazine, describes a novel symbiotic relationship between a plant and a fungus in which the fungus creates a molecular bandage laced with a fungicide to seal and protect wounds. The fungicide is the important anti-cancer drug Taxol. More generally, the paper also proposes that plants have selected for mobile microbes to inhabit their vascular tissues in order to search, swarm and kill pathogens, since plant cells themselves cannot move -- a type of convergent evolution analogous to mammalian immunity cells.
Article Impact
Press Release
Article coverage on ScienceDaily 
41._soliman_2015_current_biology.pdf
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Soliman et al (2015) article was selected as a feature Dispatch article by Current Biology  - NJ Talbot (2015) Plant immunity: A little help from fungal friends
talbot_n_2015_current_biology_soliman_highlight_paper.pdf
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Soliman et al (2015) article was selected as an Editor's Choice article by The Scientist magazine (February 2016 issue) - Click here
Soliman et al (2015) article selected as the Hot Topic by the American Society of Pharmacognosy  (The ASP Newsletter, volume 52, issue 1, year 2016) see page 13
40c._hot_topics_in_pharmacogosy_2016_soliman_p13.pdf
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39. Harding DP and Raizada MN (2015)  Alternative strategies for controlling weeds in field crop and turf systems using bacteria, fungi and viruses. Frontiers in Plant Science 6:659
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Viewed 65,000 times since publication.
40._harding_and_raizada_2015_frontiers_anti-weed_microbes_review.pdf
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38. Goron T, Bhosekar VK, Shearer C, Watts S and Raizada MN (2015) Whole plant acclimation responses by finger millet to low nitrogen stress. Frontiers in Plant Science 6:652
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39._goron_raizada_2015_frontiers_finger_millet_n_responses.pdf
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37. Thilakarathna MS and Raizada MN (2015)  A Review of Nutrient Management Studies Involving Finger Millet in the Semi-Arid Tropics of Asia and Africa. Agronomy 5: 262-290
OPEN ACCESS
38._thilakarathna_and_raizada_2015_finger_millet_nutrient_review.pdf
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36. Goron TL, Watts S, Shearer C and Raizada MN (2015) Growth in Turface clay permits root hair phenotyping along the entire crown root zone in cereal crops and demonstrates that root hair growth can extend well beyond the root hair zone. BMC Research Notes 8:143
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37._goron_2015_root_hair_bmc_research_notes.pdf
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35. Mousa WK and Raizada MN (2015) Biodiversity of genes encoding anti-microbial traits within plant associated microbes. Frontiers in Plant Science  6: 231
OPEN ACCESS
36._mousa_raizada_2015_frontiers_microbe_gene_diversity_review.pdf
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34. Goron, TL and Raizada MN (2015) Genetic diversity and genomic resources available in the small millet crops to accelerate a New Green Revolution. Frontiers in Plant Science  6: 157
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35._goron_raizada_2015_frontiers_millet_review.pdf
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33. Ettinger C, Mousa WK, Raizada MN and Eisen JA (2015) Draft Genome Sequence of Enterobacter sp. str. UCD-UG_FMILLET (Phylum Proteobacteria). Genome Announcements 3: e01461-14.
OPEN ACCESS
34._ettinger_mousa_2015_genome_announcements_finger_millet_m6.pdf
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32. Ettinger C, Shehata H, Johnston-Monje D, Raizada MN and Eisen JA (2015) Draft Genome Sequence of Burkholderia gladioli str. UCD-UG_CHAPALOTE (Phylum Proteobacteria). Genome Announcements 3: e01462-14. 
OPEN ACCESS
33._ettinger_shehata_2015_genome_announcements_a12.pdf
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31.  Johnston-Monje D., Mousa W.K., Lazarovits G and Raizada M.N. (2014) Impact of Swapping Soils on the Endophytic Bacterial Communities of Pre-Domesticated, Ancient and Modern Maize. BMC Plant Biology 14:233
OPEN ACCESS
32._johnston_monje_et_al_2014_bmc_plant_biology_soil_swap.pdf
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30. Goron, T.L. and Raizada, M.N. (2014) Current and Future Transgenic Whole-Cell Biosensors for Plant Macro- and Micro-nutrients. Critical Reviews in Plant Sciences 33: 392-413
-This comprehensive review describes novel tools to help farmers and researchers measure bioavailable soil nutrients including nitrogen
30._goron_raizada_2014_critical_reviews_plant_sciences_nutrient_biosensor_review.pdf
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29. Gaudin A.C.M., McClymont, S.A, Soliman, S.S.M. and Raizada, M.N. (2014) The Effect of Altered Dosage of a Mutant Allele of Teosinte Branched 1 (tb1-ref) on the Root System of Modern Maize. BMC Genetics 15:23
OPEN ACCESS
29._gaudin_raizada_2014_bmc_genetics_tb1.pdf
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28. Liseron-Monfils C., Bi Y.-M., Downs G.S., Wu W., Signorelli T., Lu G., Chen X., Bondo E., Zhu T., Lukens L.N., Colasanti J., Rothstein, S.J. and Raizada M.N. (2013)  Nitrogen transporter and assimilation genes exhibit developmental stage-selective expression in maize (Zea mays L.) associated with distinct cis-acting promoter motifs. Plant Signaling & Behavior  8: e26056 
OPEN ACCESS

28._liseron_monfils_raizada_2013_plant_signal_behavior_maize_n_transcriptome.pdf
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27. Bargout, R.N. and Raizada, M.N. (2013) Soil Nutrient Management in Haiti, Pre-Columbus to the Present Day: Lessons for Future Agricultural Interventions. Agriculture & Food Security ​2:11
OPEN ACCESS

-This comprehensive review on Haiti includes recommendations for inexpensive approaches to reduce synthetic nitrogen fertilizer requirements in Haiti, such as for maize (corn) farmers, including the use of rhizobia inoculants for intercropped legumes.
-The number of article views has exceeded 45,000 since publication.
27._bargout_and_raizada_2012_agric_food_security_haiti.pdf
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26. Soliman, S.S.M., Trobacher, C.P., Tsao, R., Greenwood, J. and Raizada, M.N. (2013) A Fungal Endophyte Induces Transcription of Genes Encoding a Redundant Fungicide Pathway in its Host Plant. BMC Plant Biology  13:93
OPEN ACCESS

26._soliman_raizada_2013_bmc_plant_biology_taxus_endophyte_plant_interact.pdf
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25. Berchie, J.N., Gaudin, A., McClymont, S. Raizada, M. Adu-Dapaah, H. and Sarkodie-Addo, J. (2013)  Performance of 13 Bambara Groundnut (Vigna subterranea (L) Verdc.) Landraces (from Sub-Saharan Africa) under 12 h and 14 h Photoperiod. Journal of Agronomy  12: 20-28
OPEN ACCESS
-A collaboration with the Kwame Nkrumah University of Science and Technology in Ghana (West Africa), funded by the Canadian Department of Foreign Affairs. Bambara is one of Africa's most ancient, nutritious, drought tolerant legume crops, but neglected. It effectively associates with nitrogen fixing microbes and deposits large amounts of organic nitrogen into soil and holds significant potential to combat soil degradation, climate change and malnutrition.
25._berchie_et_al_2013_j_agronomy_bambara_photoperiod.pdf
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24. Mousa, W.K. and Raizada, M.N. (2013) The diversity of anti-microbial secondary metabolites produced by fungal endophytes: An interdisciplinary perspective. Frontiers in Microbiology  4:65
OPEN ACCESS

-This review focuses on anti-pathogenic natural chemicals produced by beneficial microbes that inhabit plants.
-The article has been viewed 63,000 times since publication
24._mousa_raizada_2013_frontiers_endophyte_anti-microbe_review.pdf
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23. Liseron-Monfils, C., Lewis, T., Ashlock, D., McNicholas, P.D., Fauteaux, F., Stromvik, M. and Raizada, M.N. (2013) Promzea: A pipeline for discovery of regulatory motifs in maize and other plant species and its application to the anthocyanin and phlobaphene biosynthetic pathways and the Maize Development Atlas. BMC Plant Biology  13: 42   
OPEN ACCESS

-This paper describes a new genomics software program called Promzea that is free and available online for the research community.
23._liseron_monfils_2013_bmc_plant_biology_promzea_software.pdf
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22. Soliman, S.S.M. and Raizada, M.N. (2013) Interactions between co-habitating fungi elicit synthesis of Taxol from an endophytic fungus in host Taxus plants. Frontiers in Microbiology  4(3): 1-14    
OPEN ACCESS

-Taxol (Paclitaxel) is a natural fungicide as well as one of the world's most important anti-cancer drugs, but expensive, especially in developing nations. 
22._soliman_raizada_2013_frontiers_microbiology_taxol.pdf
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21. Nameth, M.B., Dinka, SJ, Chatfield, SP, Morris, A, English, J, Lewis, D., Oro, R. and Raizada, M.N. (2013) The shoot regeneration capacity of excised Arabidopsis cotyledons is established during the initial hours after injury and is modulated by a complex genetic network of light signalling. Plant Cell & Environment  36: 68-86.
OPEN ACCESS

In vitro plant regeneration from stem cells is important both for commercial plant biotech as well as for "low tech" efforts in developing nations to remove viruses and other pathogens by simply heating plant tissue culture planting materials, thus reducing the need for pesticides. Unfortunately, plant regeneration is very plant cultivar specific and there is considerable variability in regeneration rates. This paper explains part of the underlying problem and suggests simple, low cost strategies to move forward. 
21._nameth_2013_plant_cell_environment_arabidopsis_light.pdf
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20. Chatfield S.P., Capron R., Severino A, Penttila P.-A., Alfred S., Nahal H., Trobacher C., Raizada M.N. and Provart N.J. (2013)  Incipient stem cell niche conversion in tissue culture: using a systems approach to probe early events in WUSCHEL-dependent conversion of lateral root primordia into shoot meristems. Plant Journal  73: 798-813

20._chatfield_2013_stem_cell_regeneration_plant_j.pdf
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19. Johnston-Monje D. and Raizada M.N. (2013) A survey of diverse Zea seeds for bacterial endophytes. In: F.J. de Bruijn (ed.), Molecular Microbial Ecology of the Rhizosphere. Wiley-Blackwell. Chapter 42, p445-455.

19._johnston_monje_raizada_2013_book_chapter_proofs.pdf.zip
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18. Tessaro, M.J., Soliman, S.S.M. and Raizada, M.N. (2012) A whole cell biosensor for glutamine and applications for quantifying and visualizing glutamine in plants. Applied and Environmental Microbiology  78: 604-606.
OPEN ACCESS

This paper describes a novel nitrogen technology invented in our lab which has a number of promising applications including as a sensitive test for soil nitrogen fertilizer availability and as a potential tool for breeders to reduce the cost of breeding for more nitrogen fertilizer efficient crops.
18._tessaro_2012_appl._environ._microbiol._glnlux.pdf
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17. Taheri, A., Subramanian, J., Cline, J.A., Raizada, M.N. and Pauls, K.P. (2012) A WD-repeat gene from peach (Prunus persica L.) is a functional ortholog of Arabidopsis thaliana TRANSPARENT TESTA GLABRA1. In Vitro Cellular and Developmental Biology – Plant.  48:23-29.

17._taheri_et_al._in_vitro_2012.pdf
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16. Soliman, S.S.M., Tsao, R. and Raizada, M.N. (2011) Chemical inhibitors suggest endophytic fungal paclitaxel is derived from both mevalonate and non-mevalonate-like pathways. Journal of Natural Products  74: 2497–2504.

-First evidence that non-mevalonate enzymes exist in fungi, previously thought to only exist in bacteria and chloroplasts (plants)
-Paclitaxel (Taxol) is a natural fungicide as well as one of the world's most important anti-cancer drugs, but expensive, especially in developing nations.

16._soliman_2011_jnp_final.pdf
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15. Gaudin, A.C.M., S.A. McClymont and Raizada M.N. (2011) The nitrogen adaptation strategy of the wild teosinte ancestor of modern maize, Zea mays subsp. parviglumis. Crop Science  51: 2780-2795

-Article highlighted by the Crop Science Society of America, Agronomy Society of America and Soil Science Society of America
-2
012 Recommended "Hot Papers" by the Editorial Board of the Maize Genetics and Genomics Database (Maize GDB) 
gaudin_2011_crop_science_teosinte_n_response.pdf
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15a._gaudin_2011_crop_science_suppl_1.pdf
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14. Gaudin, A.C.M., S.A. McClymont, B.M. Holmes, E. Lyons, and Raizada M.N. (2011) Novel temporal, fine-scale and growth variation phenotypes in roots of adult-stage maize (Zea mays L.) in response to low nitrogen stress. Plant Cell & Environment  34: 2122-2137
gaudin_2011_pce_n_maize_response.pdf
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13. Johnston-Monje D. and Raizada M.N. (2011) Plant and Endophyte Relationships: Nutrient Management. In: Murray Moo-Young (ed.), Comprehensive Biotechnology, Second Edition, volume 4, pp. 713–727. Elsevier.

-This paper critically reviews the literature concerning endophytic microbes as inoculants to reduce fertilizer costs.
13._johnston_monje_raizada_2011_endophyte_review.pdf
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12. Johnston-Monje D. and Raizada M.N. (2011) Conservation and diversity of seed associated endophytes in Zea across boundaries of evolution, ethnography and ecology. PLoS One 6: e20396.
OPEN ACCESS

12._johnston_monje_and_raizada_2011_plos_one_copy.pdf
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11. Chatfield, S.P and Raizada, M.N. (2008) Ethylene and shoot regeneration: hookless1 modulates de novo shoot organogenesis in Arabidopsis thaliana. Plant Cell Reports 27: 655-666 

11._chatfield_2008_ethylene_regeneration_plant_cell_rep.pdf
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10. Dinka, S.J., Campbell, M.A., Demers, T. Raizada, M.N. (2007) Predicting the Size of the Progeny Mapping Population Required to Positionally Clone a Gene. Genetics 176: 2035-2054.
OPEN ACCESS

10._dinka_2007_positional_cloning_rice_genetics.pdf
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9. Singh PM, Wight CA, Sercinoglu O, Wilson DC, Boytsov A, Raizada M.N. (2007) Language Preferences on Websites and in Google Searches for Human Health and Food Information. Journal of Medical Internet Research 9(2):e18 
OPEN ACCESS

-A collaboration with Google Labs to measure and improve accessibility of agriculture and health information globally including in developing nations.
9._singh_2007_language_internet_jmir.pdf
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8. Dinka, S.J., and Raizada, M.N. (2006) Inexpensive fine mapping and positional cloning in plants using visible, mapped transgenes. Canadian Journal of Botany  84:179-188. 
OPEN ACCESS

8._dinka_2006_tmars_can_j_bot.pdf
File Size: 148 kb
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7. M.N. Raizada (2003) RescueMu Protocols for Maize Functional Genomics.  In Methods in Molecular Biology Vol 236: Plant Functional Genomics, Chapter 3, pp.37-58 (E. Grotewold, ed.), Humana Press, New Jersey. 

7._raizada_2003_rescuemu_plant_functional_genomics.pdf
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PhD Papers 
6. M.N. Raizada, G.-L. Nan and V. Walbot (2001)  Somatic and Germinal Mobility of the RescueMu Transposon in Transgenic Maize. Plant Cell  13, 1587-1608. 
OPEN ACCESS

•Nominated for the Best Paper of the Year Award by a Young Scientist, American Society of Plant Biologists (ASPB) 
6._raizada_2001_rescuemu_plant_cell.pdf
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5. M.N. Raizada, M.-I. Benito and V. Walbot (2001) The MuDR Transposon Terminal Inverted Repeat Contains a Complex Plant Promoter Directing Distinct Somatic and Germinal Programs.  Plant Journal  25, 79-91. 

5._raizada_2001_mutator_plantj.pdf
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4. M.N. Raizada, K.V. Brewer and V. Walbot (2001) A Maize MuDR Transposon Promoter Shows Limited Autoregulation.  Molecular and General Genomics 265, 82-94. 
4._raizada_2001_mutator_mol_genet_genomics.pdf
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3. M.N. Raizada and V. Walbot (2000) The Late Developmental Pattern of Mu Transposon Excision is Conferred by a CaMV 35S-Driven MURA cDNA in Transgenic Maize. Plant Cell  12, 5-21.  
OPEN ACCESS
3._raizada_2000_35s_mudra_plant_cell.pdf
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Undergraduate Papers

2. R.A. Bouchard, J.R.H. Frappier, L. Liu, M. Raizada, B.G. Atkinson, and D.B. Walden (1993) Developmentally-modulated Expression of Transcripts from Stress-Inducible Gene Families During Microsporogenesis and Gametophyte Development in Zea mays L.  Maydica 38, 135-144

1. B.G. Atkinson, M. Raizada, R.A. Bouchard, J.R.H. Frappier, and D.B. Walden (1993) The Independent, Stage-Specific Expression of the 18kDa Heat Shock Protein Genes During Microsporogenesis in Zea mays. Developmental Genetics 14, 15-26
1._atkinson_raizada_1993_dev_genetics_heat_shock_proteins.pdf
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Software Packages Released

Liseron-Monfils C. and Raizada M.N. (2012) Promzea: A Perl-based application to discover de novo motifs underlying co-regulated genes in maize (www.promzea.org and http://131.104.92.180/). 



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