Unlike honey bees, carpenter bees do not live in hives, they have no queen and they do not produce honey.
The work, published in the journal Molecular Ecology, focused on two species of carpenter bees, the Valley carpenter bee or Xylocopa sonorina, and the mountain carpenter bee, Xylocopa tabaniformis, from multiple geographic sites in their range, said corresponding author and community ecologist Rachel Vannette, an associate professor in the UC Davis Department of Entomology and Nematology.
The research suggests that “sociality may not be the main driver of microbiome structure in bees as is often assumed,” Vannette said.
Co-first author Madeline Handy, an undergraduate student and research intern in the Vannette laboratory and a member of the Research Scholars Program in Insect Biology (RSPIB), originated the research. Co-first author and microbiologist Dino Sbardellati of the Vannette lab and a graduate student in the UC Davis Microbiology Graduate Group, contributed bioinformatics and statistical analysis.
The researchers sequenced the microbial communities “using technology that produces longer reads from microbial DNA and allows us to get a better picture of the microbes that are found in the crop and gut, as well as their relatedness to each other,” Vannette said.
The significance of the research? “Social bees have a gut microbiome that's a model for human gut microbiomes—microbes contribute to digestion in the gut, affect host immunity and physiology in both bees and humans,” Vannette said. “But a key question is how do these types of microbiomes form and what maintains them? Social interactions has been posed as a major driver but this study suggests that advanced sociality is not required for the maintenance of this type of microbiome. Second, we show that long-read amplicon sequencing can be used in novel ways to generate hypotheses about how microbes are transmitted and maintained within insects.”
Next Steps. The next steps? “We would love to know what are these bacteria doing and if they are beneficial to bees. Our lab is excited to explore how bacterial and fungal communities in bee GI tract, stored food and other insect life stages like larvae or pupae may contribute to bee nutrition and health.”
The six-member team also included co-authors Michael Yu, UCLA Department of Ecology and Evolutionary Biology; Nicholas Saleh, Department of Entomology and Nematology Fort Lauderdale Research and Education Center, University of Florida, Davie; and Madeleine M. Ostwald, School of Life Sciences, Arizona State University, Tempe.
Their paper is titled “Incipiently Social Carpenter Bees (Xylocopa) Host Distinctive Gut Bacterial Communities and Display Geographical Structure as Revealed by Full-Length PacBio 16S rRNA Sequencing.”
“The gut microbiota of bees affects nutrition, immunity and host fitness, yet the roles of diet, sociality and geographical variation in determining microbiome structure, including variant-level diversity and relatedness, remain poorly understood. Here, we use full-length 16S rRNA amplicon sequencing to compare the crop and gut microbiomes of two incipiently social carpenter bee species, Xylocopa sonorina and Xylocopa tabaniformis, from multiple geographical sites within each species' range. We found that Xylocopa species share a set of core taxa consisting of Bombilactobacillus, Bombiscardovia and Lactobacillus, found in >95% of all individual bees sampled, and Gilliamella and Apibacter were also detected in the gut of both species with high frequency. The crop bacterial community of X. sonorina comprised nearly entirely Apilactobacillus with occasionally abundant nectar bacteria. Despite sharing core taxa, Xylocopa species' microbiomes were distinguished by multiple bacterial lineages, including species-specific variants of core taxa. The use of long-read amplicons revealed otherwise cryptic species and population-level differentiation in core microbiome members, which was masked when a shorter fragment of the 16S rRNA (V4) was considered. Of the core taxa, Bombilactobacillus and Bombiscardovia exhibited differentiation in amplicon sequence variants among bee populations, but this was lacking in Lactobacillus, suggesting that some bacterial genera in the gut may be structured by different processes. We conclude that these Xylocopa species host a distinctive microbiome, similar to that of previously characterized social corbiculate apids, which suggests that further investigation to understand the evolution of the bee microbiome and its drivers is warranted.”
Handy, who is pursuing her master's degree in public health, says her interest is “in all things microbiome, but I'm particularly interested in women's health and nutrition when it comes to the microbes living in our bodies.”
Sbardellati is interested in understanding how microbial ecology shapes macroscale ecology. In the Vannette lab, he studies bacteriophage (viruses which target bacteria) communities associated with the bumble bee gut and how phages shape gut microbial communities.
The Vannette lab is a team of entomologists, microbiologists, chemical ecologists, and community ecologists trying to understand how microbial communities affect plants and insects, and sometimes other organisms as well.
Sales, on track to receive his bachelor's degree in biotechnology (with an emphasis on plant biotechnology) in June 2022, submitted his successful research application on “Toward a More Resistant Plant: Uncovering Plant Host Targets of Novel Plant Parasitic Nematode Effectors.” He is one of only four students to be awarded the summer fellowship.
“Ado is a highly gifted student with a strong interest in agriculture and plant biology,” said Siddique. “I have really enjoyed one-on-one interaction with Ado and I have observed him growing academically and intellectually. He has a level of maturity in his research, including contributing ideas for troubleshooting, that I had no hesitations about giving him the space to continue his project independently. The IIFH fellowship program will add to his personal and professional growth and contribute to the experience of first-generation immigrant students like himself.”
ILFH awards Undergraduate Research Center Fellowships (URC-IIFH) to faculty-guided undergraduate students who perform research related to food, agriculture and health. Each fellow receives a summer research stipend, and funds for travel and/or research supplies. The fellows also will participate in professional development and entrepreneurship training, including the on-campus Entrepreneurship Academy. They will present their research results at the annual IIFH Innovator Summit in spring 2022, with opportunities to participate in the UC Davis Little Bang poster competition and the Big Bang competition.
His research involves RNA extraction, cDNA synthesis, Polymerase Chain Reaction (PCR), and gel electrophoresis, as well as GreenGate Cloning of plant parasitic nematodes genes. His skills also include seed germination and nematode hatching for plant-nematode assays, and the microscopic evaluation of nematode damage on plants.
Sales' journey to the Siddique lab began in May 2019 when he was selected a research scholar in the campuswide program, Research Scholar in Insect Biology (RSPIB), launched by UC Davis Entomology and Nematology faculty Jay Rosenheim, Joanna Chiu and Louie Yang to provide undergraduates with a closely-mentored research experience in biology. Students join in their first or second year and are placed in a faculty mentor's laboratory where they receive ongoing training and career guidance in research and scientific writing. They also learn how to present their research results at professional scientific meetings and to prepare applications for graduate or professional schools.
When Sales learned that Rosenheim, a UC Davis distinguished professor of entomology, also co-leads RSPIB, “I knew that I should apply to this program to gain more research experience and valuable connections with professors in campus.”
Sales said he chose the Siddique lab because “I found his research impactful, engaging, and unique. As someone who has always been fascinated by agriculture and plant biotechnology, I found plant parasitic nematode research as an important field of research that is underestimated and unexplored. I wanted to be part of this research because I think I would have more room to grow as a researcher and a student.”
He initially worked in the Siddique lab with postdoctoral researcher Henok Yimer. “At first, I had zero lab experience and knowledge, so I had to be intentional and attentive when it came to following lab procedures and lab experiments such as PCR or gel electrophoresis. Gradually, I became familiar with the basic assays and techniques and when Fall 2020 came, I was given my very first independent research. My research involved the identification of plant host targets of plant parasitic nematode effector proteins using cloning and microscopy techniques.”
With assistance from Siddique, Sales learned of the URC-IIFH summer fellowship and submitted a research summary, innovation statement, and letters of recommendation. An interview followed. “I was fortunate to be awarded this fellowship,” he said, “and continue my research in Dr. Siddique's lab to learn and do competent research.”
Born and raised in Manila, the Philippines, Sales moved to the United States as a teen and is a graduate of Dougherty Valley High School, San Ramon. He serves as a student intern at the UC Davis Bulosan Center for Filipino Studies to help preserve the oral history of Filipino-Americans in the Greater Sacramento Area.
He is also vice president of the UC Davis French Club; a member of the Pilipinx Americans in Science and Engineering; and the UC Davis representative to the Cornell Institute for Digital Agriculture Hackathon, which explores what technology can do for agriculture.
Murray, who anticipates receiving her bachelor of science degree in evolution, ecology and biodiversity in June 2021, is one of 396 students selected from a national pool of 5000 sophomores and juniors to receive a scholarship from the Barry Goldwater Scholarship and Excellence in Education Foundation, a federally endowed agency honoring the late senator and “designed to foster and encourage outstanding students” who are pursuing research careers in natural sciences, engineering and mathematics.
The honor includes a monetary prize of $7500. “Goldwater Scholars have impressive academic and research credentials that have garnered the attention of prestigious post-graduate fellowship programs,” according to a foundation spokesperson. Goldwater Scholars have received 93 Rhodes scholarships, 146 Marshall scholarships, 170 Churchill scholarships, 109 Hertz fellowships, and numerous other distinguished awards, including National Science Foundation Graduate Research Fellowships.
Murray, who joined the Karban lab in 2018, is a member of the campuswide Research Scholars Program in Insect Biology (RSPIB), founded and directed by three UC Davis Department of Entomology and Nematology faculty members (Jay Rosenheim, distinguished professor; Joanna Chiu, vice chair and associate professor; and Louie Yang, associate professor) to provide "academically strong and highly motivated undergraduates" with multi-year experience in biological research. The program pairs students with faculty mentors.
In the Karban lab, Murray designs and conducts independent research on plant development, flowering, and communication. She generates questions, creates protocols, collects and analyzes data.
In addition, Naomi works with UC Davis Professor Jay Stachowicz at the Bodega Marine Laboratory, where she does independent research on seagrass disease ecology, specifically herbivore-plant-pathogen interaction. She formerly worked as a full-time undergraduate researcher on seagrass ecology in the Stachowicz lab.
Native of San Diego
Naomi was born and raised in San Diego and is the first scientist in her family. Her father holds a bachelor of science degree in engineering and works as a home inspector and her mother is a newly retired lawyer.
“My interest in ecology started in high school, when I interned at the San Diego Zoo,” Naomi related. “Before the internship, I knew I loved animals and the environment, but I had no idea how I could turn those passions into a career--I thought if I liked animals, my only options were to be a zookeeper or a vet. The internship exposed me to a lot of other professionals and researchers working to protect nature, which was really my first glimpse into ecology and conservation."
"When I selected ecology, evolution, and biodiversity as my major, I intended to be primarily animal-focused, but that changed when I went to the Botanical Conservatory on UC Davis Biodiversity Museum Day my freshman year. I absolutely fell in love with it, and I interned there that spring. It turned into employment and since then, my love for plants has really grown; they're the main subject of my research now!”
Naomi is one of two Goldwater Scholars from UC Davis; the other is Jayashri Viswanathan, who seeks a doctorate in neuroscience and plans to teach biological sciences at the college level. They are among 32 recipients statewide.
Career in Forest Ecology
Naomi is leaning toward a research career in forest ecology, studying how trees affect community function and resilience “with the goal of minimizing the impacts of climate change.” She worked three weeks as a field technician on a project monitoring tree mortality in the forests of Yosemite Valley, where she tent-camped without running water or electricity, and collected data for 10 hours a day.
She acknowledged that after a few days there, she didn't know if she could meet the challenges. “But as the days passed, I realized that even when I was at my most uncomfortable, I was asking questions about the system, proposing new hypotheses for old phenomena, and marveling at the beauty of the forest,” she wrote in her essay, part of the Goldwater Scholarship application.
“As the world changes and becomes increasingly interconnected, we are in desperate need of critical thinkers, synthesizers, and people able to approach complex problems with broad, interdisciplinary perspectives,” Murray wrote. “I am working to become one of these pioneers and intend on pursuing a career in research to monitor, track, and minimize the impacts of climate change. Specifically, I plan to focus on forest ecology and how patterns of resource allocation and carbon storage among trees affect community function and ecosystem resilience.”
After receiving her bachelor's degree, Naomi plans to pursue a doctorate in ecology. “My current major prepares me with a strong foundation in basic science, and I have taken it upon myself to seek out diverse research experiences in both field and lab settings to develop a multi-dimensional perspective on critical issues in ecology,” she noted. “My time as a field technician has prepared me for ecological field work. Living as a full-time undergraduate researcher gave me a glimpse into conducting research as a career and made me familiar with work beyond the field. Additionally, participation in the Research Scholars Program in Insect Biology, a long-term pairing of undergraduates with faculty mentors to conduct research, has fostered connections instrumental in my path towards a successful research career. Perhaps most importantly, my independent design and execution of three experiments has taught me how to ask and test scientific questions.”
Murray earlier received a UC Davis Provost's Undergraduate Fellowship of $1200, a Regents Scholarship of $30,000, and a Bodega Marine Lab Undergraduate Research Fellowship of $5000, among other honors and awards.
Active in SEEDS
The Goldwater Scholar is active in Strategies for Ecology Education, Diversity, and Sustainability (SEEDS), an offshoot of the Ecological Society of America, and serves as an officer of the Davis SEEDS Chapter. The group seeks to make ecology more accessible to underrepresented groups of students. The club fosters science exploration and guidance through career panels and research facility tours.
“When I attended the 2018 SEEDS National Field Trip, the student group was mainly women of color,” Murray related in her essay. “I listened to them speak about the racism that structures this nation and its higher institutions, creating foundational issues of access to opportunity, mentorship, and funding. It was a wake-up call, making me aware of my privilege and inspiring me to deconstruct the walls that exist in my academic sphere.”
“I became an officer for the UC Davis SEEDS chapter. Through the club, I work to organize graduate student and career panels, amplifying underrepresented stories and connecting students with mentors who have similar backgrounds. I plan field trips and study sessions, and promote campus opportunities. And I help apply for funding to make all our activities equal access. Moving forward in my career I will continue this work, grateful that SEEDS has pushed me to become an active participant in scientific advancement through social justice.”
Her research expertise involves molecular genetics of animal behavior, circadian rhythm biology, and posttranslational regulation of proteins.
By using Drosophila melanogaster as a model to study the mechanisms that regulate circadian clocks, Chiu has discovered new insights into the function of key proteins that control animal circadian clocks. In particular, she has identified new mechanisms that slow down or speed up the internal clock of fruit flies and mechanisms that allow the internal clock to interpret food as timing cues--research that could help lead the way to alleviate human circadian disorders.
“Dr. Chiu is a prolific, phenomenal and talented scholar whose research is innovative, cutting-edge and groundbreaking,” said Helene Dillard, dean of the College of Agricultural and Environmental Sciences.
Steve Nadler, professor and chair of the Department of Entomology and Nematology, describes her as “a rising star.”
In announcing the Chancellor's Fellows, Chancellor Gary S. May said: “They've clearly made a mark both at UC Davis and within the academy generally. I have no doubt their contributions will continue to grow.” Each will retain the title for five years and receive a prize of $25,000 earmarked for research or scholarly work. Private donations to the UC Davis Annual Fund and the UC Davis Parents' Fund finance the program.
Chiu joined the Department of Entomology and Nematology in 2010 as an assistant professor and advanced to associate professor and vice chair in 2016. She received her bachelor's degree in biology and music from Mount Holyoke College, Mass., and her doctorate in molecular genetics in 2004 from New York University, New York. She served as a postdoctoral fellow from 2004 to 2010 in chronobiology (biological rhythms and internal clocks)--molecular genetics and biochemistry--at the Center for Advanced Biotechnology and Medicine, at Rutgers, the State University of New Jersey.
Major grants from the National Institutes of Health and the National Science Foundation fund Chiu's biological rhythms research.
In addition to her research in biological rhythms, Chiu also aims to leverage her expertise in genomics to address key issues in global food security. She is the principal investigator (PI) or co-PI on six grant awards from the State of California to research various fruit crops damaged by the spotted-wing Drosophila. At the time of her nomination, her publication record included 41 journal publications and book chapters, one U.S. Patent, and more than 3,235 journal citations (Google Scholar).
Chiu targets the spotted wing drosophila, Drosophila suzukii, first detected in North America in central California in August 2008. A native of Southeast Asia, the invasive species has already caused billions of dollars in damage to U.S. agriculture. Chiu took the lead role in sequencing the genome and is now heavily involved in finding new and more sustainable strategies to control the pest.
Chiu instigated the drive to obtain genomic data prior to its adaptation to a variety of local environments, which can differ in climate, pesticide use, natural enemies and types of fruits available. She played a leading role in establishing the SpottedWingFlyBase, a publicly available web portal documenting a variety of genomic databases for this species.
Chiu co-founded and co-directs (with professor Jay Rosenheim and associate professor Louie Yang) the campuswide Research Scholars Program in Insect Biology, launched in 2011 to provide undergraduates with a closely mentored research experience in biology. The program's goal is to provide academically strong and highly motivated undergraduates with a multi-year research experience that cultivates skills that will prepare them for a career in biological research.
Under her tutelage, many of Chiu's students are first authors of publications in prestigious journals. She continues to provide guidance and advice to undergraduate and graduate students and those who have embarked on their careers.
Former UC Davis graduate student Kelly Hamby, now assistant professor/Extension specialist in the Department of Entomology, University of Maryland, said Chiu “is so generous of her time and advice. Her office is always open to students, whether they are visiting high school students, undergraduates, or graduate students, her own students or someone else's. She carefully guides students throughout their experiments, directly providing technical training—side by side at the bench—while developing their critical thinking and communication skills. Joanna not only imparts excellent analytic and laboratory molecular skills to her students, but also commits to providing ongoing professional advice and development. Joanna's mentorship continues long after graduate and she leaves a lasting impression on students.”
“Joanna's teaching philosophy is clearly targeted towards the professional development of her students, modeling assignments on the activities of practicing scientists,” Hamby added.
The previous recipient from the Department of Entomology and Nematology was pollination ecologist Neal Williams, now a professor.
See list of this year's Chancellor's Fellows on UC Davis Dateline.
Eligible to apply are first and second-year students and new transfer students interested in a one-on-one training and mentorship in insect biology.
The program can provide the opportunity to learn research skills in all areas of biology, including behavior and ecology, biodiversity, agroecology, population biology, mathematical biology, human health, cell biology, biochemistry and molecular biology, said co-director and co-founder Jay Rosenheim, professor of entomology, Department of Entomology and Nematology, UC Davis.
Details are at http://ucanr.org/sites/insectscholars/
West, majoring in biochemistry and molecular biology, works in the Chiu lab on the Spotted Wing Drosophila (Drosophila suzukii or SWD), a serious pest of fruit crops. In collaboration with scientists in the U.S. and around the world, including Frank Zalom, UC Davis professor of entomology, West is surveying populations of SWD using next-generation sequencing to determine the extent of possible insecticide resistance.
West was one of eight students among a pool of 50 selected to be a member of the Class of 2013, Research Scholars in Insect Biology Program.