An international team of 10 scientists, led by plant nematologist Shahid Siddique, a former research group leader at the University of Bonn, Germany, and now an assistant professor in the UC Davis Department of Entomology and Nematology, has discovered the role of a plant's endodermal barrier system in defending against plant-parasitic nematodes.
“We discovered that the integrity of the endodermis—a specialized cell layer that surrounds the vascular system and helps regulate the flow of water, ions and minerals--is important to restrict nematode infection,” said Siddique, who joined the UC Davis faculty in March after serving several years at the University of Bonn.
“We found that having defects in endodermis make it easier for parasites to reach the vascular cylinder and establish their feeding site. Although, this finding is a result of basic research, it opens new avenues to for breeding resistance against cyst nematodes in crops.”
The research, “Root Endodermal Barrier System Contributes to Defence against Plant‐Parasitic Cyst and Root‐Knot Nematodes,” is published in the July 19th edition of The Plant Journal.
Siddique collaborated with scientists from Germany, Switzerland and Poland: Julia Holbein, Rochus Franke, Lukas Schreiber and Florian M. W. Grundler of the University of Bonn; Peter Marhavy, Satosha Fujita, and Niko Geldner of the University of Lasuanne, Switzrland; and Miroslawa Górecka and Miroslaw Sobeczak of the Warsaw University of Life Sciences, Poland.
“Plant-parasitic nematodes are among the most destructive plant pathogens, causing agricultural losses amounting to $80 billion annually in the United States,” said Siddique. “They invade the roots of almond, tomato, beets, potato or soybeans and migrate through different tissues to reach the central part—the vascular cylinder--of the root where they induce permanent feeding sites.”
“These feeding sites are full of sugars and amino acids and provide the parasite all the nutrients they need,” Siddique explained. “A specialized cell layer called the endodermis surrounds the vascular system and helps regulates the flow of water, ions and minerals into and out of it. However, the role of endodermis in protecting the vascular system against invaders such as nematodes had remained unknown.”
In their abstract, the scientists noted that plant-parasitic nematodes (PPN) “cause tremendous yield losses worldwide in almost all economically important crops. The agriculturally most important PPNs belong to a small group of root‐infecting sedentary endoparasites that includes cyst and root‐knot nematodes. Both cyst and root‐knot nematodes induce specialized long‐term feeding structures in root vasculature from which they obtain their nutrients.”
“A specialized cell layer in roots called the endodermis, which has cell walls reinforced with suberin deposits and a lignin‐based Casparian strip (CS), protects the vascular cylinder against abiotic and biotic threats,” the researchers explained. “Until now, the role of the endodermis, and especially of suberin and the CS, during plant–nematode interactions was largely unknown.”
The team analyzed the role of suberin and CS during interaction between Arabidopsis plants and two sedentary root parasitic nematode species, the cyst nematode Heterodera schachtii and the root‐knot nematode Meloidogyne incognita. “We found that nematode infection damages endodermis leading to the activation of suberin biosynthesis genes at nematode infection sites.”
The research was funded by a grant from the German Research Foundation.
Rebecca Godwin won first in the poster competition for her research on trapdoor spiders and Lacie Newton won second for her oral presentation on species delimitation. Their major professor, Jason Bond, is the department's Evert and Marion Schlinger Endowed Chair in Insect Systematics.
Godwin titled her work, “Revision of New World Ummidia (Mygalomorphae, Halonoproctidae)”: Her abstract: “Ummidia is a historically taxonomically difficult group of spiders belonging to the infraorder Mygalomorphae, one of the three main lineages recognized within spiders. Mygalomorph life history and their incredibly cryptic appearance make them difficult to identify, as a result they are frequently overlooked by spider systematists. Ummidia Thorell 1875 is a wide-ranging genus of trapdoor spider found both in the Mediterranean region of the Old World and in the New World from the eastern United States south to Brazil. Taxonomic work on New World Ummidia is sparse outside of original descriptions, the most recent of which are over half a century old."
"I am revising the genus Ummidia in the Nearctic region. I have approached this taxonomic problem by examining approximately 700 specimens of Ummidia from various collections (American Museum of Natural History, Museum of Comparative Zoology, Florida State Collection of Arthropods, California Academy of Sciences, and Auburn University Museum of Natural History). Examination of museum material has seemingly confirmed the undescribed diversity of Ummidia; preliminary estimates of New World species ranging between 50 and 60, with particularly high amounts of diversity in the Florida and Virginia. This study, along with many others conducted utilizing museum collections, is indicative of the importance of natural history collections and their usefulness in discovering unknown biodiversity.”
"Previous research by Hendrixson and Bond (2005) described a new sympatric species Antrodiaetus microunicolor in the A. unicolor species complex using morphological criteria (i.e. size and setal character differences) and behavioral criteria (non-overlapping mating seasons). Subsequently, they used two molecular markers COI and 28S and discovered that A. unicolor is paraphyletic with respect to A. microunicolor. To further delineate this species complex, we implement the cohesion species concept and employ multiple lines of evidence for testing genetic exchangeability and ecological interchangeability. Our integrative approach includes extensively sampling homologous loci across the genome using a version of RADseq called 3RAD, assessing population structure across their geographic range, and evaluating ecological similarity by niche-based distribution modeling. Based on our analyses, we conclude that this species complex has two or three species in addition to A. microunicolor.”
Godwin holds two degrees from Auburn University: her bachelor's degree in zoology in 2004, and her master's degree in wetland biology in 2011. She began her doctoral studies at Auburn University in 2014, and transferred to UC Davis when Bond accepted the UC Davis position in 2018.
Godwin's research interests include taxonomy, systematics, and phylogreography of trapdoor spiders, as well as effective science communication and increasing general science literacy.
Newton received her bachelor of science degree from Millsaps College, Jackson, Miss., in 2016, and then joined the Auburn University doctoral program. Like Godwin, she transferred to UC Davis with her major professor in 2018. Newton served as an undergraduate teaching assistant at Millsaps College for “Introduction to Cell Biology” and “General Zoology,” and as a graduate teaching assistant in “Introduction to Biology” at Auburn University.
Newton now serves as a graduate teaching assistant at UC Davis for “Introduction to Biology: Biodiversity and the Tree of Life.” She won the 2019-2020 George H. Vansell Scholarship, UC Davis. Her research interests include systematics, species delimitation, and phylogeography of spiders; phylogenetics; comparative transcriptomics of troglophilic and troglobitic spiders; cave biology and conservation.
Both Godwin and Newton volunteer at the Bohart Museum of Entomology's programs on spiders and at the campuswide UC Davis Biodiversity Museum Day.
Bond joined the UC Davis faculty after a seven-year academic career at Auburn University, Ala. He served as professor of biology and chair of the Department of Biological Sciences from January 2016 to July 2018, and as curator of arachnids and myriapods (centipedes, millipedes, and related animals) at the Auburn University Museum of Natural History, from August 2011 to July 2018.
Shahid Masood Siddique has never met a plant parasitic nematode he didn't like--to study, that is.
Plant-parasitic nematodes are microscopic worms that extract water and nutrients from such host plants as wheat, soybeans, sugar beets and bananas.
“They're one of the most destructive agricultural pests,” says Siddique, an assistant professor with the UC Davis Department of Entomology and Nematology. “The agricultural losses due to plant-parasitic nematodes reach an estimated $80 billion. The high impact of plant parasitic nematodes in economically important crops is not only due to the direct damage but also because of the role of some species as virus vectors.”
“In fact, a recent expert-based assessment of crop health lists nematodes among the most damaging pests and pathogens in different crops. In particular for soybeans, nematodes are the most damaging pests in the United States and around the world.”
Siddique, who joined the UC Davis faculty in March after serving as a research group leader for several years at the University of Bonn, Germany, says nematodes are troubling in other ways as well. “Although nematode-resistance varieties are available for various crops, there is an emergence of resistant-breaking population throughout the world. An example is the recent arrival of peach root-knot nematode in California, which has the potential to seriously harm many of region's important crops including almonds, peaches, eggplants, sugar beets and cucumber.”
Siddique was among a team of scientists from Bonn University and University of Missouri, who demonstrated the ability of parasitic nematodes to synthesize and secrete a functional plant hormone to manipulate the host system and establish a long-term parasitic interaction. PNAS published the research in August 2015. In a subsequent article headlined “Researchers Discover Key Link in Understanding Billion-Dollar Pests in Agriculture,” Science Daily called nematodes “a huge threat to agriculture, causing billions in crop losses every year …The discovery will help to develop crop plants that feature enhanced protection against this type of parasites.”
Born and reared in Multan, Pakistan, Siddique received two degrees in Multan: his bachelor of science degree from the Government College Bosan Road in 2001 and his master's degree in botany from the Bahauddin Zakariya University in 2004. Then it was off to Vienna, Austria to receive his doctorate in 2009 in agriculture and biotechnology from the University of Natural Resources and Life Sciences.
What sparked his interest in nematology? While studying for his masters, he developed a keen interest in molecular biology and biotechnology. For his doctorate, he sought a lab where “I could do my PhD and learn more about cell and molecular biology.” He found that opportunity with Florian Grundler, a professor at the University of Natural Resources and Life Sciences (BOKU), Vienna, Austria.
“His group was working on understanding the molecular aspects of plant-nematode interaction,” Siddique recalled. “In particular, they were using microarrays to study the changes in gene expression in plants upon nematode infection. I found the work very interesting and joined his lab.”
Nematodes did not immediately trigger his interest. “They have a complicated life cycle and infection pattern,” he points out. “Also, it is not yet possible to genetically transform plant-parasitic nematodes. So, I was mostly focusing on plants, which are more amenable to genetic manipulations. Then I gradually started to realize that how fascinating it is to work with nematodes, how they have mastered the ability to manipulate the defense and developmental pathways of their host.”
By the time he completed his doctorate, “I was completely infected by nematodes.” He still is.
What drew him to UC Davis? “High academic reputation in field of agriculture was the main factor that drew me to UC Davis,” Siddique says. “Ethnic diversity and liberal culture of golden state are some of the other factors that contributed to my decision to move to UC Davis.”
“For the next six months, I will be focusing on establishing a state-of-the art nematology lab here at UC Davis. This includes buying equipment, hiring the staff, establishing the protocol, and multiplying the nematode culture. In terms of research, my mid-term goal is understanding the plant immune responses to nematode infections. In long-term, I would like to use this knowledge to produce durable and broad-spectrum resistance in crops.”
“Another area where I will be focusing is development of molecular diagnostic tools for plant-parasitic nematodes from soil,” Siddique says. “I will be particularly focusing on nematodes that are relevant to California agriculture. Lastly, I am highly interested in understanding the mechanism of biocontrol of plant-parasitic nematodes. I expect that this will help in understanding why application of microbial biocontrol is so inconsistent.”
Siddique describes himself as “a result-oriented person and I am comfortable leading a large research team. At the same time, I like to delegate the responsibilities. My working style is collaborative and I believe on open and frank communication.”
In his leisure time, he enjoys cooking, outdoor adventures and watching documentaries. What would people be surprised to know about him? “I am an introvert,” he says. “A couple of other things: I like super spicy food and my favorite game is cricket. And oh, yes, I don't like ice-cold water.”
Siddique is currently seeking “undergraduate and graduate students to work on a number of exciting projects.”
“California is a beautiful place to live,” Siddique says, “and Davis is a perfect place to work on nematodes. So, for those interested in working with nematodes, drop me an email at firstname.lastname@example.org.”
- “Worm Subverts Plant Attack,” The Scientist, April 3, 2014
- “Researchers Discover Key Link in Understanding Billion-Dollar Pests in Agriculture,” Science Daily, Sept. 29, 2015
- “Arabidopsis Leucine-Rich Repeat Receptor–Like Kinase NILR1 Is Required for Induction of Innate Immunity to Parasitic Nematodes,” PLOS Pathogens, April 13, 2017
They received their degrees at an afternoon ceremony on Sunday, June 16 in The Pavilion, sharing the ceremony with other graduating students from the College of Agricultural and Environmental Sciences (CA&ES). CA&ES held two commencement ceremonies; one in the morning at 9 and one in the afternoon at 2.
Dean Helene Dillard and Chancellor Gary May both delivered speeches. It was a day "filled with commencement regalia, beaming smiles and other memories that will last a lifetime," May recalled on a UC Davis website.
The entomology graduates (UC Davis does not offer a major in nematology but does offer a minor) are:
- Darian Buckman
- Abram Estrada
- Lohitashwa Garikipati
- Rayanh Gutierrez
- Jo Hsuan Kao
- Eliza Litsey
- Jessica Nguyen
- Dingyuan Peng
- Jesus Martinez Rodriguez
- Matthew Salvador
- Michelle Tam
- Seiji Yokota
CA&ES was the only college or school holding two ceremonies to accommodate the graduating students. The others ceremonies:
- School of Medicine — 10 a.m. Friday, May 17, Mondavi Center
- School of Law — 11 a.m. Saturday, May 18, Mondavi Center
- School of Veterinary Medicine — 3:30 p.m Friday, May 24, Mondavi Center
- School of Education — 4 p.m. Wednesday, June 12, Mondavi Center
- Betty Irene Moore School of Nursing — 10 a.m. Thursday, June 13, Mondavi Center
- Graduate Studies — 3 p.m. Thursday, June 13, The Pavilion
- College of Biological Sciences — 9 a.m. Friday, June 14, The Pavilion
- College of Engineering — 2 p.m. Friday, June 14, The Pavilion
- College of Letters and Science — 9 a.m., and 2 and 7 p.m. Saturday, June 15, The Pavilion
- Graduate School of Management — 10 a.m. Saturday, June 15, Mondavi Center
Female golden orbweavers--tropical spiders known for weaving golden-hued webs as wide as five feet in diameter--are sometimes 10 times larger and 100 times heavier than their male counterparts, says Jason Bond, professor and Schlinger Chair in Insect Systematics, UC Davis Department of Entomology and Nematology. And notoriously, the huge females cannibalize the tiny males.
“Sexual size dimorphism (SSD) often seems to be correlated with extreme morphological, behavioral and life history phenotypes in either sex,” says Bond, senior author of a newly published paper in the Journal of Systematic Biology, a peer-reviewed scientific journal published by Oxford University Press on behalf of the Society of Systematic Biologists.
Through phylogenomic (the intersection of the fields of evolution and genomics) and comparative analyses, Bond and his colleagues found that golden orbweavers “ignore biological rules.”
The global team of 11 scientists--from Slovenia, China, Taiwan, Czech Republic and the United States (UC Davis, Smithsonian Institution, University of Idaho, University of Florida and University of Vermont)--unraveled a complex evolution of sexual size and dimorphism and found that Nephilid female gigantism is a “phylogenetically ancient phenotype, over 100 million years old, though their magnitudes vary by lineage.”
The spiders belong to the genus Nephila and family Nephilidae; the members are known for constructing huge or exaggerated webs. The species thrive in warmer regions throughout the world, including Australia, Asia, Africa (including Madagascar) and the America. One species, N. clavipes, is found in southern United States, from Texas to North Carolina.
For the paper, “Golden Orbweavers Ignore Biological Rules: Phylogenomic and Comparative Analyses Unravel a Complex Evolution of Sexual Size Dimorphism,” the team tested two biological rules: Cope's rule and Rensch's rule. Cope's rule postulates that population lineages tend to increase in body size over evolutionary time. Rensch's rule is a biological rule on allometric patterns of male and female size. Neither rule applied to the golden orbweavers.
First, the scientists established the backbone phylogeny of Nephilidae, using 367 anchored hybrid enrichment markers, and then combined these data with classical markers for a reference species level phylogeny.
“Second, we used the phylogeny to test Cope and Rensch's rules, sex specific size optima, and the coevolution of web size, type, and features with female and male body size and their ratio, SSD,” they wrote in their abstract. “Male, but not female, size increases significantly over time, and refutes Cope's rule. Allometric analyses reject the converse, Rensch's rule. Male and female body sizes are uncorrelated. Female size evolution is random, but males evolve toward an optimum size (3.2–4.9 mm). Overall, female body size correlates positively with absolute web size. However, intermediate-sized females build the largest webs (of the hybrid type), giant female Nephila and Trichonephila build smaller webs (of the aerial type), and the smallest females build the smallest webs (of the arboricolous type).”
In conclusion, the scientists proposed a new clade, a group of organisms evolving from a common ancestor. They resurrected the family Nephilidae and proposed the new clade, Orbipurae, to contain Araneidae Clerck 1757, Phonognathidae Simon 1894, new rank, and Nephilidae.
The researchers proposed “taxonomic changes based on the criteria of clade age, monophyly and exclusivity, classification information content, and diagnosability. Spider families, as currently defined, tend to be between 37 million years old and 98 million years old, and Nephilidae is estimated at 133 million years old, thus deserving family status.”
“Nephilid female gigantism is a phylogenetically ancient phenotype (over 100 million years old), as is extreme sexual size dimorphism, though their magnitudes vary by lineage,” they wrote. “Despite the sometimes conflicting trends seen within Nephilidae, the clade stands as the most extreme example of female-biased SSD among terrestrial animals, as far as we know.”
The Jason Bond lab and the Chris Hamilton lab, Department of Entomology, Plant Pathology and Nematology at the University of Idaho, Moscow, provided the anchored hybrid enrichment data and phylogenomic analysis.
Co-authors of the paper, in addition to Bond and Hamilton, are
- Matjaž Kuntner of the National Institute of Biology, Ljubljana, Slovenia; the National Museum of Natural History, Smithsonian Institution, Washington D.C.; and Hubei University, China;
- Ren-Chung Cheng, Biological Institute ZRC SAZU, Ljubljana, Slovenia, and National Chung Hsing University, Taiwan;
- Matjaž Gregorič, Nik Lupše and Tjaša Lokovšek, all with the Biological Institute ZRC SAZU, Ljubljana,Slovenia (Lupse is also affiliated with the Charles University, Prague, Czech Republic);
- Emily Moriatry Lemmon and Alan Lemmon, Florida State University, Tallahassee;
- Ingi Agnarsson of the National Museum of Natural History, Smithsonian Institution; and University of Vermont, Burlington; and
- Jonathan Coddington, National Museum of Natural History, Smithsonian Institution.
The research drew funds from Slovenian Research Agency grants, from the U.S. State Department through a Fulbright visiting scholar; ZRZ Director's Fund, National Science Foundation, Doctoral Dissertation Improvement Grant and funds from Auburn University, Alabama. Bond joined the UC Davis faculty in July of 2018 from Auburn University after a seven-year academic career there, where he served as professor of biology and chaired the Department of Biological Sciences. He also curated the arachnids and myriapods (centipedes, millipedes, and related animals) at the Auburn University Museum of Natural History.