About

Thomas Isakeit, Ph.D., is a professor and extension specialist in the Department of Plant Pathology at Texas A&M University. He holds a Ph.D. in Plant Pathology from Michigan State University, earned in 1988. His professional focus is on the management of plant diseases, with particular emphasis on diseases affecting field crops such as cotton, corn, and sorghum, as well as some vegetables, notably watermelons. His work involves responding to the plant disease problems faced by Texas growers through research and educational efforts. He aims to anticipate how future changes in agriculture will influence plant diseases and their control strategies. A key component of his role is communicating research findings effectively to farmers and other clientele to help maintain the viability of agriculture in Texas. His activities are centered on solving practical plant disease issues and providing extension services to support agricultural productivity.

Research topics

• Biology
• Agronomy
• Artificial Intelligence
• Computer Science
• Genetics
• Horticulture
• Ecology
• Engineering
• Virology
• Agricultural engineering
• Geography
• Veterinary medicine
• Botany
• Remote sensing

Selected publications

• Economic quantification of the potential yield loss from Helicoverpa zea1 feeding on corn ears

  Southwestern Entomologist · 2025-08-28 · 1 citations

  article

  Resumen. Cuantificacón Económica de la Pérdida Potencial del Rendimiento del Maíz por el Daño de Helicoverpa zea1 a la Mazorca El gusano elotero, Helicoverpa zea, (Boddie), es una plaga importante de maíz (Zea mays) en el sur de Estados Unidos, que se alimenta de las granos de maíz lo que reduce el rendimiento. En los últimos cuatro años, se ha clasificado entre las cinco plagas más dañinas para el maíz de campo en Estados Unidos y Canadá Aunque Cry1Ab se considera ineficaz contra el gusano elotero debido a la resistencia desarrollada en el gusano elotero debido a la resistencia desarrollada en el campo, Vip3Aa sigue siendo eficaz. Se simuló el daño a la cosecha en el cultivar de maíz Viptera®, que expresa las proteínas Bt Cry1Ab + Vip3Aa, para determinar la relación entre y la alimentación del gusano elotero y la pérdida de rendimiento en ausencia de compensación por la pecute;rdida de grano por parte de la planta, y para determinar el beneficio económico del uso de maíz que expresa Vip3Aa. El beneficio económico de ultilizar maíz que expresa Vip3Aa depende de la densidad de siembra, el valor de mercado del maíz, y el nivel de daño causado por la alimentación del gusano elotero. Nuestro modelo de beneficio económico sugiere que a un precio de mercado de $196.84/tonelada ($5.00/bu), beneficio econoómico del maíz que expresa Vip3Aa se produce con un daño de alimentación de 2.5 cm2 para densidades de siembra de 59,304 semillas/ha (24,00 semillas/ac), y 74,131 semillas/ha (30,00 semillas/ac).

  PublisherDOI

• Integrated metabarcoding and culture-dependent assessments reveal Pseudomonas as dominant hyphosphere-pathobiont in Race 4 Fusarium wilt pathogen of cotton

  Frontiers in Microbiology · 2025-09-04 · 1 citations

  articleOpen access

  The hyphosphere, the microhabitat surrounding fungal hyphae, hosts complex microbial interactions that can influence fungal biology, yet the microbial community in hyphospheres of pathogenic fungi are seldom characterized. In this study, we investigated the hyphosphere of Fusarium oxysporum f. sp. vasinfectum Race 4 (FOV4), a major fungal pathogen threatening cotton, to characterize its bacterial community and assess potential functional roles. An integrated approach was employed combining confocal time-lapse microscopy, 16S rRNA metabarcoding, culture-dependent bacterial isolation, whole genome sequencing, and fungal-bacterial coculture assays. Microscopy confirmed hyphosphere association, and the bacterial predisposition towards the growing hyphal tips. Metabarcoding showed a stable hyphosphere community dominated by a single Pseudomonas ASV accounting for over 95% of relative abundance, with strong negative correlations to most other taxa. To evaluate the functions, ten representative bacterial isolates were sequenced, revealing enrichment in metabolic pathways related to carbon, nitrogen, and sulfur cycling. In particular, Pseudomonas laurylsulfatiphila showed high counts of oxidoreductases and hydrolases. Coculture assays demonstrated that several bacterial isolates significantly promoted FOV4 hyphal extension, while having limited or inconsistent effects on other Fusarium strains, indicating strain-specific interactions. Together, the findings reveal a stable and functionally enriched bacterial community in the FOV4 hyphosphere, with potential implications for fungal fitness and virulence. These results support the emerging concept of a hyphosphere-pathobiome and highlight microbial associations as targets for future plant disease management strategies.

  PublisherOA PDFDOI

• Estimated Soybean Yield and Economic Losses Caused by Diseases in the United States and Ontario, Canada, from 2020 to 2024

  Plant Health Progress · 2025-11-21

  article

  The impact of plant diseases on soybean ( Glycine max [L.] Merrill) yield was estimated across 29 states and Ontario, Canada, from 2020 to 2024 by university and government plant pathologists. Losses from 29 pathogens or groups of pathogens were estimated at the end of each growing season through a survey and summarized across years and locations. Diseases reduced soybean yield by an estimated 1.2 billion bushels (32.8 million metric tons) valued at 14.6 billion USD for the survey period. Per acre, this estimated mean economic loss was equal to 32.93 USD (81.37 USD per hectare) across all locations and years, excluding costs such as fungicide seed treatments and foliar applications. Soybean cyst nematode (SCN) ( Heterodera glycines Ichinohe) reduced yield by 482.4 million bushels (13.1 million metric tons), a value nearly four times greater than the next greatest cause of yield loss, which was sudden death syndrome (SDS) (caused by Fusarium virguliforme O'Donnell & T. Aoki). Following SCN and SDS, the most significant yield losses were attributed to white mold (caused by Sclerotinia sclerotiorum [Lib.] de Bary), seedling diseases (caused by various pathogens), Phytophthora root and stem rot (caused by Phytophthora sojae Kaufm. & Gerd.), and root-knot nematodes ( Meloidogyne spp.), in descending order. The most important diseases in the southern United States were generally different from those in the northern United States and Ontario. The data presented here will enable government agencies, scientists, educators, commodity groups, funding organizations, and plant breeders to enhance and prioritize policy, research, funding, and education regarding soybean disease management.

  PublisherDOI

• Summer cover crop mixtures: Part 1—Establishment and biomass potential of diverse mixes

  Agronomy Journal · 2025-09-01

  article

  Abstract Cover crop mixtures combine species from different functional groups to optimize specific agronomic goals and address resource concerns. This study investigated four summer cover crop mixtures, specifically examining their establishment, growth, biomass production, and overall species suitability within the mix. Mix 1 was a grass‐only blend comprising four grass species. Mix 2 included two grasses, one legume, and one nonlegume broadleaf. Mix 3 consisted of two grasses and two legumes, while Mix 4 contained two legumes and two nonleguminous broadleaf plants. Sorghum‐sudangrass ( Sorghum bicolor × S. bicolor var . sudanense ) and pearl millet ( Pennisetum glaucum L.) were the main biomass contributors in Mixes 1, 2, and 3, with an average share of 98.4%, 87.7%, and 81.6%, respectively. Mix 1 had less than 12% plant population establishment due to the poor emergence of foxtail ( Setaria italica L.) and proso millet ( Panicum miliaceum L.). Mixes 2, 3, and 4 had the greatest plant population densities. Mix 4, which did not include any grass species, produced the least biomass; sunn hemp ( Crotalaria juncea L.) was the greatest biomass contributor in this mix, accounting for 71.5% of the biomass. Overall, mixes that contained grasses and legumes performed better in terms of establishment success and biomass production. Soil moisture availability during establishment was a crucial factor for the emergence and establishment success of summer mixes, especially for small‐seeded species. Mixes 2 and 3, containing grasses and legumes, produced the greatest biomass and can be a valuable addition to rotations in the southern region.

  PublisherDOI

• Corn Yield Loss Estimates Due to Diseases in the United States and Ontario, Canada, from 2020 to 2023

  Plant Health Progress · 2025-11-05

  article

  Corn ( Zea mays L.) was planted on 375.1 million acres (151.8 million hectares) cumulative from 2020 to 2023 in the United States and Ontario, Canada. During these 4 years, 59.6 billion bushels (1.5 billion metric tons) of grain were produced, valued at 325.9 billion U.S. dollars (USD). Plant pathogens that cause diseases limit annual grain production and reduce associated economic returns while also increasing management costs to prevent potential losses. Plant pathologists representing 29 U.S. states and Ontario, Canada, were asked to estimate annual percent yield losses caused by 37 pathogens or pathogen groups through an online survey. Grain contaminated by mycotoxins was also estimated. According to survey results, estimated overall annual percent losses ranged from negligible in Texas in 2023 to 15.8% in Michigan in 2021 and averaged 3.0% across all surveyed regions for the 4-year period. Diseases reduced corn yield by an estimated 2.5 billion bushels (63.7 million metric tons) across participating locations, with tar spot (caused by Phyllachora maydis), Fusarium stalk rot (caused by Fusarium spp.), and plant-parasitic nematodes causing the most significant losses. The total estimated economic loss caused by diseases was 13.8 billion USD, and the average economic loss was 37.76 USD per acre (93.30 USD per hectare) across all years and locations. Survey data and the resulting analysis can help inform corn disease management and guide pathology education, policy, and research priorities among scientists, government representatives, Extension educators, and other stakeholders.

  PublisherDOI

• Identification of microbial communities associated with Phymatotrichopsis omnivora sclerotia in two Texas fields

  Frontiers in Microbiomes · 2025-11-28

  articleOpen accessSenior authorCorresponding

  The soilborne fungus Phymatotrichopsis omnivora causes a mid- to late-season disease known as cotton root rot (CRR). In the United States, P. omnivora is primarily found in Arizona, New Mexico, Oklahoma, and Texas in soils that are alkaline, calcareous, and rarely freeze deeply. This fungus has a wide host range, and can cause substantial losses in cotton crops. In Texas, not all cotton-producing soils have widespread CRR despite having the characteristics to support P. omnivora . Considering the lack of CRR in some Texas soils, we hypothesize that this absence could be due to the microbial composition associated with sclerotia of P. omnivora . The objective of this study was to identify the taxa that make up microbial communities associated with P. omnivora sclerotia in different soils during both the cotton-growing and off seasons. The microbiota associated with P. omnivora sclerotia were identified by burying lab-generated sclerotia in cotton-producing soils. These sclerotia were recovered, along with soil samples for metabarcoding targeting the 16S rRNA gene and the internal transcribed spacer region. When compared to bulk soil, microbial communities associated with sclerotia differed in community composition and taxa relative abundance between a soil with widespread CRR and one in which the disease is absent. Within these soil communities, potential bacterial and fungal biomarkers that reduce CRR were identified. Furthermore, microbial communities of P. omnivora sclerotia changed seasonally. This study presents the first detailed characterization of microorganisms associated with P. omnivora sclerotia in different cotton-producing soils. Our findings support the view that P. omnivora sclerotia serve as ecological hubs, shaping microbial communities with possible implications for disease suppression. Several enriched taxa are culturable, offering candidates for future biocontrol studies that could inform disease management strategies that focus on increased microbial competition.

  PublisherOA PDFDOI

• Genetic and Pathogenic Variability among Isolates of Sporisorium reilianum Causing Sorghum Head Smut

  Journal of Fungi · 2024-01-12 · 4 citations

  articleOpen access

  (L.) Moench) head smut, is present in most sorghum-producing regions. This seed replacement fungal disease can reduce yield by up to 80% in severely infected fields. Management of this disease can be challenging due to the appearance of different pathotypes within the pathogenic population. In this research, the genetic variability and pathogenicity of isolates collected from five Texas Counties was conducted. Due to the lack of available space, 21 out of 32 sequenced isolates were selected and evaluated for virulence patterns on the six sorghum differentials, Tx7078, BTx635, SC170-6-17 (TAM2571), SA281 (Early Hegari), Tx414, and BTx643. The results reveal the occurrence of a new pathotype, 1A, and four previously documented US pathotypes when the 21 isolates were evaluated for virulence patterns on the differentials. The most prevalent was pathotype 5, which was recovered from Brazos, Hidalgo, Nueces, and Willacy Counties, Texas. This pathotype was followed by 1A and 6 in frequency of recovery. Pathotype 4 was identified only from isolates collected from Hidalgo County, while pathotype 1 was from Burleson County, Texas. It appeared that the previous US head smut pathotypes (2 and 3) are no longer common, and the new pathotypes, 1A, 5, and 6, are now predominant. The phylogenetic tree constructed from the single-nucleotide polymorphism (SNP) data through the neighbor-joining method showed high genetic diversity among the tested isolates. Some of the diverse clades among the tested isolates were independent of their sampled locations. Notably, HS37, HS49, and HS65 formed a clade and were classified as 1A in the virulence study, while HS 61 and HS 66, which were collected from Nueces County, were grouped and identified as pathotype 5.

  PublisherOA PDFDOI

• Correlations among Agronomic Traits Obtained from Sorghum Accessions Planted in a Field Infected with Three Important Fungal Diseases

  Journal of Plant Studies · 2024-01-08 · 2 citations

  articleOpen access

  A total of 179 sorghum cultivars planted in replicated plots in Isabela, Puerto Rico, were evaluated for five agronomically important traits grain yield, seed weight, panicle height, panicle length, and flowering time. This study identified the top cultivars in each trait through statistical analysis. In a previous study, the reaction of the same cultivars to anthracnose, rust, grain mold, and germination rates was determined. Combining the five traits in this study and the previous four measured traits, a correlation analysis among the nine traits was conducted. The results revealed that there are significant correlations between a few paired traits. Correlations such as panicle height and rust infection (Spearman’s ρ= 0.36), panicle height and grain mold infection (Spearman’s ρ= -0.30), germination rate and panicle height (Pearson’s r= 0.31), germination rate and panicle length (Pearson’s r= 0.27), panicle length and panicle height (Pearson’s r= 0.52), flowering time and panicle height (Pearson’s r= 0.65), and flowering time and panicle length (Pearson’s r= 0.50) were found.

  PublisherOA PDFDOI

• ‘Supermelon’ and ‘Flavorific’: Two New Hybrid Muskmelon Cultivars with Resistance to Monosporascus cannonballus from Texas A&M AgriLife Research

  HortScience · 2023-06-26 · 4 citations

  articleOpen access

  "‘Supermelon’ and ‘Flavorific’: Two New Hybrid Muskmelon Cultivars with Resistance to Monosporascus cannonballus from Texas A&M AgriLife Research" published on Jul 2023 by American Society for Horticultural Science.

  PublisherOA PDFDOI

• Genetic Diversity and Classification of Colletotrichum sublineola Pathotypes Using a Standard Set of Sorghum Differentials

  Journal of Fungi · 2023-12-20 · 5 citations

  articleOpen access

  Anthracnose, incited by Colletotrichum sublineola, is the most destructive foliar disease of sorghum and, under severe conditions, yield losses can exceed 80% on susceptible cultivars. The hyper-variable nature of the pathogen makes its management challenging despite the occurrence of several resistant sources. In this study, the genetic variability and pathogenicity of 140 isolates of C. sublineola, which were sequenced using restriction site-associated sequencing (RAD-Seq), resulted in 1244 quality SNPs. The genetic relationship based on the SNP data showed low to high genetic diversity based on isolates’ origin. Isolates from Georgia and North Carolina were grouped into multiple clusters with some level of genetic relationships to each other. Even though some isolates from Texas formed a cluster, others clustered with isolates from Puerto Rico. The isolates from Puerto Rico showed scattered distribution, indicating the diverse nature of these isolates. A population structure and cluster analysis revealed that the genetic variation was stratified into eight populations and one admixture group. The virulence pattern of 30 sequenced isolates on 18 sorghum differential lines revealed 27 new pathotypes. SC748-5, SC112-14, and Brandes were resistant to all the tested isolates, while BTx623 was susceptible to all. Line TAM428 was susceptible to all the pathotypes, except for pathotype 26. Future use of the 18 differentials employed in this study, which contains cultivars/lines which have been used in the Americas, Asia, and Africa, could allow for better characterization of C. sublineola pathotypes at a global level, thus accelerating the development of sorghum lines with stable resistance to the anthracnose pathogen.

  PublisherOA PDFDOI

Frequent coauthors

• Louis K. Prom

  Southern Plains Agricultural Research Center

  31 shared

• Clint Magill

  Texas A&M University

  21 shared

• Seth C. Murray

  Texas A&M University

  17 shared

• Ramasamy Perumal

  Fort Hays State University

  17 shared

• G. N. Odvody

  14 shared

• William L. Rooney

  12 shared

• Hugo E. Cuevas

  United States Department of Agriculture

  12 shared

• Michael V. Kolomiets

  Texas A&M University

  11 shared

Education

• Ph.D., Plant Pathology

  Michigan State University

  1988