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Manish N. Raizada
Department of Plant Agriculture, University of Guelph, Guelph, Canada

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Journal article
Published: 24 June 2021 in Scientific Reports
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In corn/maize, silks emerging from cobs capture pollen, and transmit resident sperm nuclei to eggs. There are > 20 million silks per U.S. maize acre. Fungal pathogens invade developing grain using silk channels, including Fusarium graminearum (Fg, temperate environments) and devastating carcinogen-producers (Africa/tropics). Fg contaminates cereal grains with mycotoxins, in particular Deoxynivalenol (DON), known for adverse health effects on humans and livestock. Fitness selection should promote defensive/healthy silks. Here, we report that maize silks, known as styles in other plants, possess complex and dynamic microbiomes at the critical pollen-fungal transmission interval (henceforth: transmitting style microbiome, TSM). Diverse maize genotypes were field-grown in two trial years. MiSeq 16S rRNA gene sequencing of 328 open-pollinated silk samples (healthy/Fg-infected) revealed that the TSM contains > 5000 taxa spanning the prokaryotic tree of life (47 phyla/1300 genera), including nitrogen-fixers. The TSM of silk tip tissue displayed seasonal responsiveness, but possessed a reproducible core of 7–11 MiSeq-amplicon sequence variants (ASVs) dominated by a single Pantoea MiSeq-taxon (15–26% of sequence-counts). Fg-infection collapsed TSM diversity and disturbed predicted metabolic functionality, but doubled overall microbiome size/counts, primarily by elevating 7–25 MiSeq-ASVs, suggestive of a selective microbiome response against infection. This study establishes the maize silk as a model for fundamental/applied research of plant reproductive microbiomes.

ACS Style

Eman M. Khalaf; Anuja Shrestha; Jeffrey Rinne; Michael D. J. Lynch; Charles R. Shearer; Victor Limay-Rios; Lana M. Reid; Manish N. Raizada. Transmitting silks of maize have a complex and dynamic microbiome. Scientific Reports 2021, 11, 1 -17.

AMA Style

Eman M. Khalaf, Anuja Shrestha, Jeffrey Rinne, Michael D. J. Lynch, Charles R. Shearer, Victor Limay-Rios, Lana M. Reid, Manish N. Raizada. Transmitting silks of maize have a complex and dynamic microbiome. Scientific Reports. 2021; 11 (1):1-17.

Chicago/Turabian Style

Eman M. Khalaf; Anuja Shrestha; Jeffrey Rinne; Michael D. J. Lynch; Charles R. Shearer; Victor Limay-Rios; Lana M. Reid; Manish N. Raizada. 2021. "Transmitting silks of maize have a complex and dynamic microbiome." Scientific Reports 11, no. 1: 1-17.

Journal article
Published: 05 March 2021 in Agronomy
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Ground and aerial-based high throughput phenotyping platforms (HTPPs) to evaluate chlorophyll-related traits have been utilized to predict grain yield in crops including wheat (Triticum aestivum L.). This study evaluated chlorophyll-related and other physiological and yield traits in a panel of 318 Nepali spring wheat genotypes, termed the Nepali Wheat Diversity Panel (NWDP). Field experiments were conducted using an alpha-lattice design in Nepal and Canada. Chlorophyll-related traits were evaluated with a Soil Plant Analysis Development (SPAD) meter and the normalized difference vegetation index (NDVI) using a handheld GreenSeeker and an Unmanned Aerial Vehicle (UAV). Relative leaf epicuticular waxiness was recorded using visual assessments. There was a significant positive association (p < 0.001) between waxiness and SPAD-based chlorophyll estimates, and both of these traits displayed a significant positive relationship with grain yield. However, unexpectedly, NDVI derived from both GreenSeeker and UAV was negatively associated with waxiness and grain yield. The results obtained after segregating the trait means into groups based on waxiness scores and breeding history of genotypes indicated that waxiness along with precipitation could be affecting the multispectral reflectance. These results suggest that caution should be taken when evaluating a large and diverse wheat population for leaf chlorophyll using high-throughput NDVI methods.

ACS Style

Kamal Khadka; Andrew Burt; Hugh Earl; Manish Raizada; Alireza Navabi. Does Leaf Waxiness Confound the Use of NDVI in the Assessment of Chlorophyll When Evaluating Genetic Diversity Panels of Wheat? Agronomy 2021, 11, 486 .

AMA Style

Kamal Khadka, Andrew Burt, Hugh Earl, Manish Raizada, Alireza Navabi. Does Leaf Waxiness Confound the Use of NDVI in the Assessment of Chlorophyll When Evaluating Genetic Diversity Panels of Wheat? Agronomy. 2021; 11 (3):486.

Chicago/Turabian Style

Kamal Khadka; Andrew Burt; Hugh Earl; Manish Raizada; Alireza Navabi. 2021. "Does Leaf Waxiness Confound the Use of NDVI in the Assessment of Chlorophyll When Evaluating Genetic Diversity Panels of Wheat?" Agronomy 11, no. 3: 486.

Review article
Published: 15 December 2020 in Frontiers in Sustainable Food Systems
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There is a general unawareness of food crops indigenous to the African continent that have contributed to Western culture. This under-appreciation is particularly relevant in the current context of societal movements to end historic racism and value the contributions of peoples of African origin and African skin colors. Lack of awareness of the contributions of Africa's crops has negative practical consequences, including inadequate investments in preserving and maximizing the use of crop diversity to facilitate breeding. This paper provides an overview and analysis of African crops that have made significant contributions to the United States and globally, and/or hold potential in the twenty-first century. The paper specifically discusses watermelon, coffee, kola, rooibos, oil palm, shea, cowpea/black eyed pea, leafy greens, okra, yam, sorghum, pearl millet, finger millet, teff, and fonio. The review focuses on the intersection of these crops with racialized peoples, with a particular focus on African-Americans starting with slavery. The analysis includes the sites of domestication of African crops, their historical migration out of Africa, their sociocultural contributions to cuisines and products around the world, their uses today, and the indigenous knowledge associated with traditional cultivation and landrace selection. The untapped potential of local genetic resources and indigenous agronomic strategies are also described. The review demonstrates that African crops played an important role in the development of American cuisine, beverages and household products. Many of these crops are nutritious, high value and stress tolerant. The paper concludes that African crops hold significant promise in improving the resiliency of global food production systems, to mitigate climate change and alleviate food insecurity and rural poverty, especially in dry regions of the world. It is hoped that this review contributes to teaching the next generation of agriculturalists, food scientists and international development professionals about the valuable contributions of Africa's resilient crops and peoples.

ACS Style

Emily C. Sousa; Manish N. Raizada. 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 2020, 4, 1 .

AMA Style

Emily C. Sousa, Manish N. Raizada. 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. 2020; 4 ():1.

Chicago/Turabian Style

Emily C. Sousa; Manish N. Raizada. 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, no. : 1.

Journal article
Published: 20 November 2020 in Sustainability
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Printed pictures are traditional forms of agricultural extension for smallholder farmers. They receive historical academic criticism but remain inexpensive, do not require technical skills (unlike smartphones), and bypass language/literacy barriers. Here, a comprehensive participatory pipeline is described that included 56 Nepalese women farmer editors to develop 100 picture-based lessons. Thereafter, the Theory of Planned Behavior is used as a framework to evaluate 20 diverse lessons using quantitative and qualitative data (Nvivo-11) collected from four groups, focusing on low-literacy women: the women farmer editors (n = 56); smallholder field testers who had prior exposure to extension agents and the actual innovations (control group, n = 120), and those who did not (test group, n = 60); expert stakeholders (extension agents/scientists, n = 25). The expected comprehension difference between farmer groups was non-substantive, suggesting that the participatory editing/testing approaches were effective. There were surprising findings compared to the academic literature: smallholders comprehended the pictures without the help of extension agents, perhaps because of the participatory approaches used; children assisted their mothers to understand caption-based lessons; the farmers preferred printed pictures compared to advanced information and communication technologies (ICTs); and the resource-poor farmers were willing to pay for the printed materials, sufficient to make them cost-neutral/scalable. These findings have implications for smallholder farmers beyond Nepal.

ACS Style

Rachana Devkota; Helen Hambly Odame; John Fitzsimons; Roshan Pudasaini; Manish Raizada. Evaluating the Effectiveness of Picture-Based Agricultural Extension Lessons Developed Using Participatory Testing and Editing with Smallholder Women Farmers in Nepal. Sustainability 2020, 12, 9699 .

AMA Style

Rachana Devkota, Helen Hambly Odame, John Fitzsimons, Roshan Pudasaini, Manish Raizada. Evaluating the Effectiveness of Picture-Based Agricultural Extension Lessons Developed Using Participatory Testing and Editing with Smallholder Women Farmers in Nepal. Sustainability. 2020; 12 (22):9699.

Chicago/Turabian Style

Rachana Devkota; Helen Hambly Odame; John Fitzsimons; Roshan Pudasaini; Manish Raizada. 2020. "Evaluating the Effectiveness of Picture-Based Agricultural Extension Lessons Developed Using Participatory Testing and Editing with Smallholder Women Farmers in Nepal." Sustainability 12, no. 22: 9699.

Journal article
Published: 01 May 2020 in Phytochemistry
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Taxol is a cytotoxic agent against various types of cancers. The cytotoxic activities of Taxol can be extended to its synthesizing plant. Here, Taxol is shown to have special synthesis, storage and transport mechanisms that avoid the toxic effects on its source plant. The sites of Taxol biosynthesis, transport and storage were revealed by quantification of plant Taxol, its intermediate baccatin III, the polyphenol side chain precursor , gene expression analysis of the major Taxol biosynthetic genes and in situ immuno-labeling. Although the biosynthesis of Taxol was limited by the expression of its biosynthetic genes and the presence of baccatin III, its presence did not correlate to baccatin III accumulation, nor to the expression of biosynthetic genes. However, Taxol presence positively correlated to polyphenol accumulation (late stage in Taxol assembly) and the resin-like hydrophobic bodies (HB, storage organelles). These results indicate that the presence of Taxol requires two complementary steps, biosynthesis followed by storage. Each step is limited by the availability of different precursors, which differ in their localization within the plant. Thus, the sites of biosynthesis, transport and storage of Taxol are different. Taxus media (Rehder) plant wood showed high concentrations of baccatin III and the expression of biosynthetic genes. However, the concentrations of Taxol, polyphenol and HB were very high in the plant outer layers including phloem and dead bark (rhytidome). Furthermore, in situ immuno-labeling showed that taxadiene synthase (the rate-limiting enzyme in Taxol biosynthesis) was mainly found in the wood, while Taxol primarily localized to the outer tissues. Conclusively, wood can be considered as the site of Taxol biosynthesis. Our data also propose that Taxol then accumulates into HB in order to permit its transport within the living plant tissues without causing toxic effects. This is followed by Taxol storage in the outer tissues including phloem and dead bark.

ACS Style

Sameh S.M. Soliman; Manish N. Raizada. Sites of biosynthesis and storage of Taxol in Taxus media (Rehder) plants: Mechanism of accumulation. Phytochemistry 2020, 175, 112369 .

AMA Style

Sameh S.M. Soliman, Manish N. Raizada. Sites of biosynthesis and storage of Taxol in Taxus media (Rehder) plants: Mechanism of accumulation. Phytochemistry. 2020; 175 ():112369.

Chicago/Turabian Style

Sameh S.M. Soliman; Manish N. Raizada. 2020. "Sites of biosynthesis and storage of Taxol in Taxus media (Rehder) plants: Mechanism of accumulation." Phytochemistry 175, no. : 112369.

Review
Published: 07 March 2020 in Sustainability
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Cover crops provide a range of well-documented benefits to growers and the environment. However, no single species can deliver all of these benefits, and hence planting mixtures is gaining increasing attention. To the best of our knowledge, there is no comprehensive review on different multi-mix strategies. This article reviews available studies on multi-mixes, focusing on temperate North America, and discusses objective criteria for selecting components of a multi-mix and what future research is needed. Very few peer-reviewed studies on multi-mixes are currently available; a diversity of species compositions is being tested with a wide range of potential benefits but also with various limitations. Selection of species in multi-mixes is based on different criteria that help improve multiple ecosystem services. An emerging concept is the importance of selecting cover crop species with functional complementarity rather than simply increasing the number of species. Based on this concept, objective criteria have been developed to select the species for a multi-mix: grower objectives/primary purpose of planting the cover crop, crop rotation and cropping system compatibility, above and belowground compatibility, complementarity of different ecosystem functions, compatibility with the growing environment, duration for cover crop growth, termination option(s) available, input/labour costs, planting equipment required, persistence/weediness, and potential net economic returns. We propose a step-wise procedure to develop effective multi-species mixtures. The number of species and their ratio in the mixtures will depend on objective criteria, and hence long-term research is required to assess different species compositions and their impacts.

ACS Style

Tejendra Chapagain; Elizabeth A. Lee; Manish N. Raizada. The Potential of Multi-Species Mixtures to Diversify Cover Crop Benefits. Sustainability 2020, 12, 2058 .

AMA Style

Tejendra Chapagain, Elizabeth A. Lee, Manish N. Raizada. The Potential of Multi-Species Mixtures to Diversify Cover Crop Benefits. Sustainability. 2020; 12 (5):2058.

Chicago/Turabian Style

Tejendra Chapagain; Elizabeth A. Lee; Manish N. Raizada. 2020. "The Potential of Multi-Species Mixtures to Diversify Cover Crop Benefits." Sustainability 12, no. 5: 2058.

Journal article
Published: 02 January 2020 in Sustainability
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Agricultural mechanization in developing countries has taken at least two contested innovation pathways—the “incumbent trajectory” that promotes industrial agriculture, and an “alternative pathway” that supports small-scale mechanization for sustainable development of hillside farming systems. Although both pathways can potentially reduce human and animal drudgery, the body of literature that assesses the sustainability impacts of these mechanization pathways in the local ecological, socio-economic, cultural, and historical contexts of hillside farms is either nonexistent or under-theorized. This paper addresses this missing literature by examining the case of Nepal’s first Agricultural Mechanization Promotion Policy 2014 (AMPP) using a conceptual framework of what will be defined as “responsible innovation”. The historical context of this assessment involves the incumbent trajectory of mechanization in the country since the late 1960s that neglected smallholder farms located in the hills and mountains and biased mechanization policy for flat areas only. Findings from this study suggest that the AMPP addressed issues for smallholder production, including gender inequality, exclusion of smallholder farmers, and biophysical challenges associated with hillside farming systems, but it remains unclear whether and how the policy promotes small-scale agricultural mechanization for sustainable development of agriculture in the hills and mountains of Nepal.

ACS Style

Rachana Devkota; Laxmi Prasad Pant; Hom Nath Gartaula; Kirit Patel; Devendra Gauchan; Helen Hambly-Odame; Balaram Thapa; Manish N. Raizada. Responsible Agricultural Mechanization Innovation for the Sustainable Development of Nepal’s Hillside Farming System. Sustainability 2020, 12, 374 .

AMA Style

Rachana Devkota, Laxmi Prasad Pant, Hom Nath Gartaula, Kirit Patel, Devendra Gauchan, Helen Hambly-Odame, Balaram Thapa, Manish N. Raizada. Responsible Agricultural Mechanization Innovation for the Sustainable Development of Nepal’s Hillside Farming System. Sustainability. 2020; 12 (1):374.

Chicago/Turabian Style

Rachana Devkota; Laxmi Prasad Pant; Hom Nath Gartaula; Kirit Patel; Devendra Gauchan; Helen Hambly-Odame; Balaram Thapa; Manish N. Raizada. 2020. "Responsible Agricultural Mechanization Innovation for the Sustainable Development of Nepal’s Hillside Farming System." Sustainability 12, no. 1: 374.

Journal article
Published: 12 January 2019 in Agriculture
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Studies have shown the potential of rhizobia and associated micronutrients to enhance symbiotic nitrogen fixation in legumes. Tens of millions of smallholder farmers, however, farm on mountain hillsides in highly variable soil and microenvironments, with different crop rotations, inputs and cultural practices. Here, on the terraces of the Nepalese Himalayas, we evaluated rhizobium inoculants (local, exotic), micronutrients (molybdenum, boron) and their combinations as technologies for smallholder farmers under highly variable microenvironments and traditional practices. The study was conducted as a series of participatory on-farm trials with 39 terrace farmers in two mid-hill districts of Nepal (Dhading, Kaski) from 2015 to 2017. Plots were measured for relevant agronomic traits. As expected, when comparing treatment plots with adjacent control plots within each farm, the results demonstrated tremendous farm-to-farm variability for nodulation, vegetative biomass, shoot nitrogen content, grain yield, and grain N content. Despite the variation observed, the data showed that the number of farms that showed yield increases from the rhizobium interventions, compared to those that suffered yield losses, was generally 2:1. We discuss potential experimental and socio-agronomic reasons for the variable results, including rainfall, which appeared critical. The results demonstrate the promise of rhizobium interventions for hillside smallholder farmers, even in a highly variable context.

ACS Style

Malinda S. Thilakarathna; Tejendra Chapagain; Bhawana Ghimire; Roshan Pudasaini; Bir Bhahadur Tamang; Khem Gurung; Khem Choi; Laxmi Rai; Samjhana Magar; Bishnu Bk; Shankar Gaire; Manish N. Raizada. 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 2019, 9, 20 .

AMA Style

Malinda S. Thilakarathna, Tejendra Chapagain, Bhawana Ghimire, Roshan Pudasaini, Bir Bhahadur Tamang, Khem Gurung, Khem Choi, Laxmi Rai, Samjhana Magar, Bishnu Bk, Shankar Gaire, Manish N. Raizada. 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. 2019; 9 (1):20.

Chicago/Turabian Style

Malinda S. Thilakarathna; Tejendra Chapagain; Bhawana Ghimire; Roshan Pudasaini; Bir Bhahadur Tamang; Khem Gurung; Khem Choi; Laxmi Rai; Samjhana Magar; Bishnu Bk; Shankar Gaire; Manish N. Raizada. 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, no. 1: 20.

Research article
Published: 01 January 2019 in Phytobiomes Journal
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Forage legumes experience defoliation from grazing and injury in both natural and agricultural ecosystems. Defoliation induces rhizodeposition of nitrogen (N) compounds from root systems that can feed microbes and plants that depend on the rhizosphere. The literature suggests that N exudates are primarily released from root tips, and those from legume nodules are released via slow nodule decomposition. However, the early timing and precise locations of N release postdefoliation are poorly characterized. The objectives of this study were to directly image tissue-specific N exudation sites in forage legumes, specifically for glutamine, and to do so at early time points postdefoliation. Glutamine is the primary assimilate of symbiotic nitrogen fixation in nodules and a key transport form of fixed N in amide-exporting legumes. Three amide-exporting forages, alfalfa (Medicago sativa), red clover (Trifolium pretense), and white clover (Trifolium repens), were defoliated or not, and placed on agar embedded with whole cell biosensor cells (GlnLux) that detect glutamine. There were two unexpected findings. First, Gln release occurred rapidly, starting within 2 h postdefoliation, depleting rapidly. Second, the sources of early Gln release were primarily nodules in addition to the expected young lateral roots/root tips. Lux quantification statistically confirmed the key findings. These observations suggest that N exudate release should be added to the list of defoliation stress early responses in nodules, and may have implications for our understanding of how defoliation impacts the rhizosphere microbiome. Furthermore, GlnLux-agar imaging represents a new assay to explore the proposed but yet unknown mechanisms underlying organic N exudation in plants.

ACS Style

Malinda S. Thilakarathna; Manish N. Raizada. A Biosensor-Based Assay (GlnLux-Agar) Shows Defoliation Triggers Rapid Release of Glutamine from Nodules and Young Roots of Forage Legumes. Phytobiomes Journal 2019, 3, 85 -91.

AMA Style

Malinda S. Thilakarathna, Manish N. Raizada. A Biosensor-Based Assay (GlnLux-Agar) Shows Defoliation Triggers Rapid Release of Glutamine from Nodules and Young Roots of Forage Legumes. Phytobiomes Journal. 2019; 3 (2):85-91.

Chicago/Turabian Style

Malinda S. Thilakarathna; Manish N. Raizada. 2019. "A Biosensor-Based Assay (GlnLux-Agar) Shows Defoliation Triggers Rapid Release of Glutamine from Nodules and Young Roots of Forage Legumes." Phytobiomes Journal 3, no. 2: 85-91.

Article
Published: 25 October 2018 in Microbiology Resource Announcements
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Presented here is the draft genome sequence of Enterobacter cloacae 3D9. This candidate seed endophyte was isolated from Zea nicaraguensis .

ACS Style

Christopher R. Dumigan; Gregory E. Perry; K. Peter Pauls; Manish N. Raizada. Draft Genome Sequence of Enterobacter cloacae 3D9 (Phylum Proteobacteria). Microbiology Resource Announcements 2018, 7, e00902-18 .

AMA Style

Christopher R. Dumigan, Gregory E. Perry, K. Peter Pauls, Manish N. Raizada. Draft Genome Sequence of Enterobacter cloacae 3D9 (Phylum Proteobacteria). Microbiology Resource Announcements. 2018; 7 (16):e00902-18.

Chicago/Turabian Style

Christopher R. Dumigan; Gregory E. Perry; K. Peter Pauls; Manish N. Raizada. 2018. "Draft Genome Sequence of Enterobacter cloacae 3D9 (Phylum Proteobacteria)." Microbiology Resource Announcements 7, no. 16: e00902-18.

Review
Published: 11 October 2018 in Pathogens
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Silks are the long threads at the tips of maize ears onto which pollen land and sperm nuclei travel long distances to fertilize egg cells, giving rise to embryos and seeds; however fungal pathogens also use this route to invade developing grain, causing damaging ear rots with dangerous mycotoxins. This review highlights the importance of silks as the direct highways by which globally important fungal pathogens enter maize kernels. First, the most important silk-entering fungal pathogens in maize are reviewed, including Fusarium graminearum, Fusarium verticillioides, and Aspergillus flavus, and their mycotoxins. Next, we compare the different modes used by each fungal pathogen to invade the silks, including susceptible time intervals and the effects of pollination. Innate silk defences and current strategies to protect silks from ear rot pathogens are reviewed, and future protective strategies and silk-based research are proposed. There is a particular gap in knowledge of how to improve silk health and defences around the time of pollination, and a need for protective silk sprays or other technologies. It is hoped that this review will stimulate innovations in breeding, inputs, and techniques to help growers protect silks, which are expected to become more vulnerable to pathogens due to climate change.

ACS Style

Michelle Thompson; Manish N. Raizada. Fungal Pathogens of Maize Gaining Free Passage Along the Silk Road. Pathogens 2018, 7, 81 .

AMA Style

Michelle Thompson, Manish N. Raizada. Fungal Pathogens of Maize Gaining Free Passage Along the Silk Road. Pathogens. 2018; 7 (4):81.

Chicago/Turabian Style

Michelle Thompson; Manish N. Raizada. 2018. "Fungal Pathogens of Maize Gaining Free Passage Along the Silk Road." Pathogens 7, no. 4: 81.

Journal article
Published: 16 August 2018 in Microbiology Resource Announcements
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Presented here is the draft genome sequence of Enterobacter cloacae 3F11. This seed endophyte solubilizes rock phosphate and was isolated from Zea nicaraguensis .

ACS Style

Christopher R. Dumigan; Gregory E. Perry; K. Peter Pauls; Manish N. Raizada. Draft Genome Sequence of Enterobacter cloacae 3F11 (Phylum Proteobacteria ). Microbiology Resource Announcements 2018, 7, e00846-18 .

AMA Style

Christopher R. Dumigan, Gregory E. Perry, K. Peter Pauls, Manish N. Raizada. Draft Genome Sequence of Enterobacter cloacae 3F11 (Phylum Proteobacteria ). Microbiology Resource Announcements. 2018; 7 (6):e00846-18.

Chicago/Turabian Style

Christopher R. Dumigan; Gregory E. Perry; K. Peter Pauls; Manish N. Raizada. 2018. "Draft Genome Sequence of Enterobacter cloacae 3F11 (Phylum Proteobacteria )." Microbiology Resource Announcements 7, no. 6: e00846-18.

Correction article
Published: 11 June 2018 in Frontiers in Microbiology
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ACS Style

Eman M Khalaf; Manish N. Raizada. Corrigendum: Bacterial Seed Endophytes of Domesticated Cucurbits Antagonize Fungal and Oomycete Pathogens Including Powdery Mildew. Frontiers in Microbiology 2018, 9, 1 .

AMA Style

Eman M Khalaf, Manish N. Raizada. Corrigendum: Bacterial Seed Endophytes of Domesticated Cucurbits Antagonize Fungal and Oomycete Pathogens Including Powdery Mildew. Frontiers in Microbiology. 2018; 9 ():1.

Chicago/Turabian Style

Eman M Khalaf; Manish N. Raizada. 2018. "Corrigendum: Bacterial Seed Endophytes of Domesticated Cucurbits Antagonize Fungal and Oomycete Pathogens Including Powdery Mildew." Frontiers in Microbiology 9, no. : 1.

Review
Published: 21 May 2018 in Agronomy
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Precision agriculture (PA) has been used for ≥25 years to optimize inputs, maximize profit, and minimize negative environmental impacts. Legumes play an important role in cropping systems, by associating with rhizobia microbes that convert plant-unavailable atmospheric nitrogen into usable nitrogen through symbiotic nitrogen fixation (SNF). However, there can be field-level spatial variability for SNF activity, as well as underlying soil factors that influence SNF (e.g., macro/micronutrients, pH, and rhizobia). There is a need for PA tools that can diagnose spatial variability in SNF activity, as well as the relevant environmental factors that influence SNF. Little information is available in the literature concerning the potential of PA to diagnose/optimize SNF. Here, we critically analyze SNF/soil diagnostic methods that hold promise as PA tools in the short–medium term. We also review the challenges facing additional diagnostics currently used for research, and describe the innovations needed to move them forward as PA tools. Our analysis suggests that the nitrogen difference method, isotope methods, and proximal and remote sensing techniques hold promise for diagnosing field-level variability in SNF. With respect to soil diagnostics, soil sensors and remote sensing techniques for nitrogen, phosphorus, pH, and salinity have short–medium term potential to optimize legume SNF under field conditions.

ACS Style

Malinda S. Thilakarathna; Manish N. Raizada. Challenges in Using Precision Agriculture to Optimize Symbiotic Nitrogen Fixation in Legumes: Progress, Limitations, and Future Improvements Needed in Diagnostic Testing. Agronomy 2018, 8, 78 .

AMA Style

Malinda S. Thilakarathna, Manish N. Raizada. Challenges in Using Precision Agriculture to Optimize Symbiotic Nitrogen Fixation in Legumes: Progress, Limitations, and Future Improvements Needed in Diagnostic Testing. Agronomy. 2018; 8 (5):78.

Chicago/Turabian Style

Malinda S. Thilakarathna; Manish N. Raizada. 2018. "Challenges in Using Precision Agriculture to Optimize Symbiotic Nitrogen Fixation in Legumes: Progress, Limitations, and Future Improvements Needed in Diagnostic Testing." Agronomy 8, no. 5: 78.

Developmental biology
Published: 12 February 2018 in In Vitro Cellular & Developmental Biology - Animal
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How light exposure of excised plant tissues impacts the success of subsequent adventitious root regeneration is poorly understood. Here, exposure to high light intensity was observed to inhibit root regeneration from Arabidopsis thaliana (L.) Heynh. cotyledon explants. Transfers to dark followed by high-intensity light (or reciprocal) were used to define when the explants were most light-sensitive and when adventitious root formation was most inhibited. Exposure of explants to light during the first 6–48 h after excision strongly inhibited root regeneration. Mutants and chemical inhibitors were used to identify modulators of this light-induced response. During the first 48 h post excision, reduction in photoprotective xanthophylls or application of chemicals known to promote reactive oxygen species caused the cotyledon explants to become light-hypersensitive, and decreased adventitious root regeneration. Filtering out blue/ultraviolet-A wavelengths reduced the negative effects of light, while mutants defective in phytochrome A or light-activated transcription factor ELONGATED HYPOCOTYL 5 were hypersensitive to early light exposure. A mutant defective in chalcone synthase (transparent testa 4) showed reduced root regeneration, regardless of early light or dark exposure. Application of a polar auxin transport inhibitor, 1-N-naphthylphthalamic acid, during the first 24 h post excision reduced explant light sensitivity and increased the percentage that successfully induced adventitious roots. These results indicated a critical role for light during the initial post-excision hours on root regeneration in Arabidopsis. The data suggested that complex interactions between light, photoreceptor signaling, reactive oxygen species, photoprotective pigments, and auxin act upon adventitious root induction in A. thaliana cotyledon explants.

ACS Style

M. Blair Nameth; Travis L. Goron; Stephen J. Dinka; Adam D. Morris; Jenny English; Dorrett Lewis; Rosalinda Oro; Manish N. Raizada. 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 - Animal 2018, 54, 273 -290.

AMA Style

M. Blair Nameth, Travis L. Goron, Stephen J. Dinka, Adam D. Morris, Jenny English, Dorrett Lewis, Rosalinda Oro, Manish N. Raizada. 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 - Animal. 2018; 54 (3):273-290.

Chicago/Turabian Style

M. Blair Nameth; Travis L. Goron; Stephen J. Dinka; Adam D. Morris; Jenny English; Dorrett Lewis; Rosalinda Oro; Manish N. Raizada. 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 - Animal 54, no. 3: 273-290.

Original research article
Published: 05 February 2018 in Frontiers in Microbiology
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The cucurbit vegetables, including cucumbers, melons and pumpkins, have been cultivated for thousands of years without fungicides. However, their seed germination stage is prone to be infected by soil-borne fungal and oomycete pathogens. Endophytes are symbionts that reside inside plant tissues including seeds. Seed endophytes are founders of the juvenile plant microbiome and can promote host defense at seed germination and later stages. We previously isolated 169 bacterial endophytes associated with seeds of diverse cultivated cucurbits. We hypothesized that these endophytes can antagonize major fungal and oomycete pathogens. Here we tested the endophytes for in vitro antagonism (dual culture assays) against important soil-borne pathogens (Rhizoctonia solani, Fusarium graminearum, Phytophthora capsici, Pythium aphanideratum). The endophytes were also assayed in planta (leaf disk and detached leaf bioassays) for antagonism against a foliar pathogen of global importance, Podosphaera fuliginea, the causative agent of cucurbit powdery mildew. The endophytes were further tested in vitro for secretion of volatile organic compounds (VOCs) known to induce plant defense. Extracellular ribonuclease activity was also tested, as a subset of pathogenesis-related (PR) proteins of plant hosts implicated in suppression of fungal pathogens, displays ribonuclease activity. An unexpected majority of the endophytes (70%, 118/169) exhibited antagonism to the five phytopathogens, of which 68% (50/73) of in vitro antagonists belong to the genera Bacillus and Paenibacillus. All Lactococcus and Pantoea endophytes exhibited anti-oomycete activity. However, amongst the most effective inoculants against Podosphaera fuliginea were Pediococcus and Pantoea endophytes. Interestingly, 67% (113/169) of endophytes emitted host defense inducing VOCs (acetoin/diacetyl) and 62% (104/169) secreted extracellular ribonucleases in vitro, respectively. These results show that seeds of cultivated cucurbits package microbes with significant disease-suppression potential. As seeds can act as vectors for genetic transmission of endophytes across host generations, it is interesting to hypothesize whether humans, when selecting seeds of healthy hosts, may have inadvertently selected for disease-suppressing seed endophytes. As the majority of pathogen-suppressing endophytes belong to Bacillus and Paenibacillus, and since Bacilli are widely used as commercial biocontrol agents of vegetables, we propose that these agents are mimicking the ecological niche established by their endophytic cousins.

ACS Style

Eman M Khalaf; Manish N. Raizada. Bacterial Seed Endophytes of Domesticated Cucurbits Antagonize Fungal and Oomycete Pathogens Including Powdery Mildew. Frontiers in Microbiology 2018, 9, 42 .

AMA Style

Eman M Khalaf, Manish N. Raizada. Bacterial Seed Endophytes of Domesticated Cucurbits Antagonize Fungal and Oomycete Pathogens Including Powdery Mildew. Frontiers in Microbiology. 2018; 9 ():42.

Chicago/Turabian Style

Eman M Khalaf; Manish N. Raizada. 2018. "Bacterial Seed Endophytes of Domesticated Cucurbits Antagonize Fungal and Oomycete Pathogens Including Powdery Mildew." Frontiers in Microbiology 9, no. : 42.

Research article
Published: 01 January 2018 in Phytobiomes Journal
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Microbial symbiotic nitrogen fixation (SNF) occurs inside root nodules, where fixed-N (NH4+) from rhizobia is first assimilated into the amino acid glutamine (Gln). Visualization of Gln dynamics in nodulated root systems of different plant species would require re-engineering transgenic Gln reporters specific for each rhizobia/host genotype. Here we demonstrate the use of companion biosensor cells called GlnLux (Escherichia coli auxotrophic for Gln and constitutively expressing lux) to image Gln accumulation in nodulated root systems across a diversity of legume/rhizobia species. Companion GlnLux cells are embedded into agar (GlnLux agar) upon which legume root systems are placed following freeze-thawing to cause Gln leakage. Photons released from nearby activated biosensor cells are captured using a photon capture camera. Using split root systems, we demonstrate that in diverse amide-exporting legumes (alfalfa, lentil, and green pea) and a ureide-exporting legume (soybean) that GlnLux agar imaging is sufficiently sensitive to detect Gln release from individual nodules and can differentiate root systems with active nif+ from inactive nif− nodules. The assay permits visualization of both source and sink dynamics of nodule Gln, specifically, Gln import into nodules from roots (for nodule growth and/or amino acid cycling), Gln assimilated from fixed nitrogen that accumulates inside nodules, and Gln export from nodules into roots from this assimilatory-N. GlnLux agar-based imaging is thus a new research tool to localize the accumulation and transfer of a critical amino acid required for rhizobia symbionts within legume phytobiomes. We discuss the ability of this technology to open new frontiers in basic research and its limitations.

ACS Style

Malinda S. Thilakarathna; Manish N. Raizada. Visualizing Glutamine Accumulation in Root Systems Involved in the Legume–Rhizobia Symbiosis by Placement on Agar Embedded with Companion Biosensor Cells. Phytobiomes Journal 2018, 2, 117 -128.

AMA Style

Malinda S. Thilakarathna, Manish N. Raizada. Visualizing Glutamine Accumulation in Root Systems Involved in the Legume–Rhizobia Symbiosis by Placement on Agar Embedded with Companion Biosensor Cells. Phytobiomes Journal. 2018; 2 (3):117-128.

Chicago/Turabian Style

Malinda S. Thilakarathna; Manish N. Raizada. 2018. "Visualizing Glutamine Accumulation in Root Systems Involved in the Legume–Rhizobia Symbiosis by Placement on Agar Embedded with Companion Biosensor Cells." Phytobiomes Journal 2, no. 3: 117-128.

Short communication
Published: 06 December 2017 in Symbiosis
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Cereal crops including maize (Zea mays L.) are inhabited by non-disease causing microbes known as endophytes that can promote plant growth, aid in host nutrient acquisition and promote host pathogen resistance. Screening endophytes for beneficial traits in planta using large, slow-growing cereals is challenging, thus a rapid but relevant in planta system is needed. Here, we propose that turfgrasses can be used as high-throughput assay systems for screening cereal microbes for beneficial nutrient traits. Turfgrasses are genetic relatives of cereals, but small with fast growth rates; they can be grown in test tubes under sterile conditions on defined media. Five turfgrass genotypes were evaluated for traits ideal for assaying endophytes with nutrient acquisition traits. Based on these criteria, annual ryegrass (Lolium multiflorum) was selected as a high-throughput assay system. Annual ryegrass was then used to test a collection of maize endophytes for their ability to promote plant biomass in the absence of nitrogen. Out of 75 bacterial endophytes tested, one strain (an Enterobacter sp) consistently promoted root and shoot biomass. We discuss the potential of annual ryegrass as a model assay system to test cereal endophytes for acquisition of various nutrients, changes in root/shoot architecture as well as anti-pathogen traits.

ACS Style

Hanan Shehata; Eric M. Lyons; Manish N. Raizada. Turfgrasses as model assay systems for high-throughput in planta screening of beneficial endophytes isolated from cereal crops. Symbiosis 2017, 76, 71 -76.

AMA Style

Hanan Shehata, Eric M. Lyons, Manish N. Raizada. Turfgrasses as model assay systems for high-throughput in planta screening of beneficial endophytes isolated from cereal crops. Symbiosis. 2017; 76 (1):71-76.

Chicago/Turabian Style

Hanan Shehata; Eric M. Lyons; Manish N. Raizada. 2017. "Turfgrasses as model assay systems for high-throughput in planta screening of beneficial endophytes isolated from cereal crops." Symbiosis 76, no. 1: 71-76.

Journal article
Published: 18 October 2017 in Scientific Reports
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In the animal microbiome, localization of microbes to specific cell types is well established, but there are few such examples within the plant microbiome which includes endophytes. Endophytes are non-pathogenic microbes that inhabit plants. Root hairs are single cells, equivalent to the nutrient-absorbing intestinal microvilli of animals, used by plants to increase the root surface area for nutrient extraction from soil including phosphorus (P). There has been significant interest in the microbiome of intestinal microvilli but less is known about the root hair microbiome. Here we describe a bacterial endophyte (3F11) from Zea nicaraguensis, a wild corn discovered in a Nicaraguan swamp above rock-P lava flowing from the San Cristobal volcano. Rock-P is insoluble and a major challenge for plants. Following seed coating and germination on insoluble-P, the endophyte colonized epidermal surfaces, ultimately colonizing root hairs intracellularly. The endophyte promoted root hair growth and secreted acids to solubilize rock-P for uptake by a larger root hair surface. The most interesting observation was that a seed-coated endophyte targeted and colonized a critical cell type, root hair cells, consistent with earlier studies. The endophyte maintained its targeting ability in two evolutionary divergent hosts, suggesting that the host recognition machinery is conserved.

ACS Style

Hanan Shehata; Christopher Dumigan; Sophia Watts; Manish N. Raizada. An endophytic microbe from an unusual volcanic swamp corn seeks and inhabits root hair cells to extract rock phosphate. Scientific Reports 2017, 7, 1 -13.

AMA Style

Hanan Shehata, Christopher Dumigan, Sophia Watts, Manish N. Raizada. An endophytic microbe from an unusual volcanic swamp corn seeks and inhabits root hair cells to extract rock phosphate. Scientific Reports. 2017; 7 (1):1-13.

Chicago/Turabian Style

Hanan Shehata; Christopher Dumigan; Sophia Watts; Manish N. Raizada. 2017. "An endophytic microbe from an unusual volcanic swamp corn seeks and inhabits root hair cells to extract rock phosphate." Scientific Reports 7, no. 1: 1-13.

Methods article
Published: 09 October 2017 in Frontiers in Plant Science
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Legumes are protein sources for billions of humans and livestock. These traits are enabled by symbiotic nitrogen fixation (SNF), whereby root nodule-inhabiting rhizobia bacteria convert atmospheric nitrogen into usable nitrogen. Unfortunately, SNF rates in legume crops suffer from undiagnosed incompatible/suboptimal interactions between crop varieties and rhizobia strains. There are opportunities to test much large numbers of rhizobia strains if cost/labour-effective diagnostic tests become available which may especially benefit researchers in developing countries. Inside root nodules, fixed nitrogen from rhizobia is assimilated into amino acids including glutamine (Gln) for export to shoots as the major fraction (amide-exporting legumes) or as the minor fraction (ureide-exporting legumes). Here we have developed a new leaf punch based technique to screen rhizobia inoculants for SNF activity following inoculation of both amide exporting and ureide exporting legumes. The assay is based on measuring Gln output using the GlnLux biosensor, which consists of Escherichia coli cells auxotrophic for Gln and expressing a constitutive lux operon. Subsistence farmer varieties of an amide exporter (lentil) and two ureide exporters (cowpea and soybean) were inoculated with different strains of rhizobia under controlled conditions, then extracts of single leaf punches were incubated with GlnLux cells, and light-output was measured using a 96-well luminometer. In the absence of external N and under controlled conditions, the results from the leaf-punch assay correlated with 15N-based measurements, shoot nitrogen percentage and shoot total fixed nitrogen in all three crops. The technology is rapid, inexpensive, high-throughput, requires minimum technical expertise and very little tissue and hence is relatively non-destructive. We compare and contrast the benefits and limitations of this novel diagnostic assay compared to existing methods.

ACS Style

Malinda S. Thilakarathna; Nicholas Moroz; Manish N. Raizada. 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 2017, 8, 1 .

AMA Style

Malinda S. Thilakarathna, Nicholas Moroz, Manish N. Raizada. 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. 2017; 8 ():1.

Chicago/Turabian Style

Malinda S. Thilakarathna; Nicholas Moroz; Manish N. Raizada. 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, no. : 1.