Principal Investigator

britt

Britt Koskella: Britt is an Associate Professor in the Department of Integrative Biology at UC Berkeley. She received her PhD in 2008 from the department of Biology at Indiana University, and then did her postdoctoral work (first as an NSF International Research Fellow, then a UK NERC Research Fellow) at Oxford University, UC Santa Cruz, and then the University of Exeter.

Postdoctoral researchers

Kate Ennis: Dr Ennis joined the lab in 2020 as a UC Berkeley President’s postdoctoral Fellow, and NSF Postdoctoral fellow. She will be collaborating with Steve Lindow on a project exploring the floral microbiome and the role phages play in structuring these communities. More here!
Dominique Holtappels: After his PhD at KU Leuven with Prof. R. Lavigne focusing on phage biocontrol in multiple pathosystems, Dr. ir. Holtappels joined the Koskella lab to work on viral communities in the pear tree phyllosphere. In his research he looks at viral competition and co-evolution dynamics in the phyllosphere using two disease models as well as the effects of drought on the abundance of viral communities. More here!
Milo Johnson: Dr Johnson joined the lab in 2022 as an NSF Postdoctoral fellow. He is collaborating with Drs. Adam Arkin and Adam Deutschbauer on a project exploring the ecology and evolution of Erwinia tracheiphila, a pathogen of cucurbits. He plans to use DNA barcoding technologies to observe both population dynamics and evolutionary processes during infection. More here!
Kyle Meyer: Dr Meyer joined the group in March 2019 from Brendan Bohannan’s group at the University of Oregon. He has published broadly on the spatial ecology of microbial communities, how microbial communities drive biogeochemical functions, and how environmental change impacts microbes living in tropical soils (see here), and here his work focuses on understanding how dispersal and transmission mode shape the plant microbiome.”.

Graduate students

Mason Kamalani Chock: Kama is a graduate student in Integrative Biology and Ford Fellow interested in plant microbial communities and how we can harness them to increase disease resistance for horticultural and conservation purposes. More on his website!
Asa Conover: Asa is a PhD student in Intergrative Biology and Berkeley Fellow excited to study the ecology of plant-associated bacterial and fungal communities and how these communities shape plant fitness.
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Reena Debray: Reena is a graduate student in Integrative Biology, and NSF GRFP fellow. She is interested in using microbial communities as model systems to test ecological and evolutionary theory. See Reena’s website for more details about her ongoing research projects.
Emily Dewald-Wang: Emily joined the lab from Washington University, St. Louis in October 2019 as a research technicianto help coordinate the Pear Fire Blight Project, and in 2020 joined the lab to undertake her PhD research focused on the interaction of community and disease ecology.
Claire Evensen: Claire joined the lab in 2021 and is co-advised by Prof Mike Boots. She is broadly interested in coevolution in complex communities. Her projects utilize both wet-lab and dry-lab tools from community ecology, microbiology, epidemiology, and network theory to explore how community diversity is established and maintained.
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Elijah Mehlferber: Elijah is a graduate student in Integrative Biology who is interested in the ecology of the phyllosphere microbiome. Broadly, he wants to understand why certain bacteria associate with plants, how those associations affect the plant’s interactions with other bacteria, and how those bacteria interact with other members of the microbiome.

Research technicians and Postbaccalaureate fellows

Lab Manager
Julia Sherman
: Julia joined the lab in 2019 as an undergraduate at UC Berkeley to work with Kyle on understanding how microbiome transmission shapes host-microbe interactions. She now works as the full-time Lab Manager for both the Boots and Koskella labs.

Undergraduate researchers

Anika Bansal: Anika is working with Kama to model the dispersal patterns of ballistospore-forming fungi in the phyllosphere. She is interested in characterizing how the dispersal abilities of foliar yeast affect the assembly and composition of the plant microbiome.
Fernanda Torres: Fernanda joined the lab in 2021 to work on her honors thesis with Emily. She aims to understand the effects of acquiring resistance to phage in copper-resistant P. syringae.
George Rickus: George is pursuing a double major in Molecular & Cellular Biology and Computer Science. He is currently working on the Pear Project with Dominique, using bioinformatics to analyze the sequenced genomes of samples and making a streamlined pipeline to integrate many of these bioinformatic tools.
Jon Giller: Jon is a first year student intending to major in Chemical Engineering. He is currently working on the Pear Project with Dominique to isolate bacteriophages from Erwinia and Pseudomonas bacteria.
Serey Nouth: Serey is a third year microbial biology student interested in phages from every aspect imaginable! She is currently working on the Pear Project with Dominique and trying to understand the environmental effects on phage distribution in the pear trees in Berkeley.
Sydney Abelson: Sydney is a Microbial Biology student who joined the lab in 2021. She is working on the Pear Project with Dominique to study disease ecology and the relationships between bacteria in the pear phyllosphere.

Past lab members

Postdoctoral researchers:

Wenke Smets (2019-2021, BAEF Postdoctoral fellow): Dr. Smets joined the group in October 2019 as a B.A.E.F. Postdoctoral Fellow from Sarah Lebeer’s group at the University of Antwerp, Belgium. Her previous work focused on the impact of pollution in urban environments on the phyllosphere, and vice versa. Her time in the lab included examination of the process of phyllosphere community assembly and the functional response of these communities over the course of succession.

Graduate students:

Catherine Hernandez (2015-2021, PhD student, UC Berkeley,Integrative Biology): Dr. Hernandez completed her dissertation in Integrative Biology Department as an NSF GRFP and Berkeley fellow. Her work focused on measuring coevolutionary change between bacteria and phages living within leaves of tomato plants. She used a combination of experimental evolution and molecular approaches to test when/how the coevolutionary process differs between the in planta and in vitro environments, and how coevolution impacts upon molecular evolution of bacteria. She is now a postdoctoral fellow with Prof Paul Turner at Yale.

Norma Morella (2015-2019, PhD student, UC Berkeley, Plant and Microbial Biology): Dr Morella completed her dissertation work examining: (i) the impact of microbial transmission (e.g. via seeds or via aerial transmission) on microbiome assembly and function; (ii) novel methods to measure bacteria-phage dynamics and assess the risk of bacteriophage infection in microbial populations/communities; and (iii) the impact of phages in host-associated microbial communities. She is now a postdoctoral research fellow at the Fred Hutchinson Cancer Institute in the group of Prof. Neelendu Dey, studying the role of the microbiome in cancer.

Sean Meaden (2012-2015, PhD student, University of Exeter): Sean finished his PhD focusing on understanding how coevolution with phages affects the fitness of a bacterial pathogen on its plant host. He went on to work as a postdoctoral researcher with Prof Mike Boots at UC Berkeley, then as a postdoctoral researcher with Prof. Edze Westra, and most recently as a Marie Curie Research fellow in the lab of Prof. Peter Fineran at the University of Otago.

Research technicians:

Alina Lee (2018-2021): Alina joined the lab in 2018 as an undergraduate researcher helping on numerous projects, including leading the way in hunting for phages to complement our growing synthetic microbiome of tomato plants. She then stayed on as a full-time research technician leading the Pear project, and is now a researcher in Paul Turner’s lab at Yale.

Isabella Muscettola (2019-2021): Isabella joined the lab in 2019 as an undergraduate researcher working with Kama to characterize interactions among fungi within the phyllosphere. She then stayed on as a part-time research technician working with Kyle on a large scale microbiome passaging experiment, and is preparing to start her PhD in Microbiology.

Tristan Caro (2017-2019, Undergraduate researcher and then full-time research technician): Tristan joined the lab in 2017 to work with Britt on developing a new system to explore natural bacteria-phage dynamics during fire blight infection of pear trees. He is now undertaking his PhD work at the University of Colorado at Boulder.

Nicole Parr (2013-2015, Full-time research technician, University of Exeter; now a PhD student at the University of Exeter, working with Lucy Hawkes on bird migration). Nicole worked on measuring bacteria-phage coevolution in the horse chestnut phyllosphere (Koskella, B., & Parr, N. (2015). The evolution of bacterial resistance against bacteriophages in the horse chestnut phyllosphere is general across both space and time. Philosophical Transactions of the Royal Society B: Biological Sciences370(1675), 20140297).

Will Crowther (2014, Research assistant based at Oxford University; now a research technician at Warwick University) Will worked with Jessica Metcalf and Britt on a project exploring the role of the microbiome in tree health (Koskella, B., Meaden, S., Crowther, W. J., Leimu, R., & Metcalf, C. J. E. (2017). A signature of tree health? Shifts in the microbiome and the ecological drivers of horse chestnut bleeding canker disease. New Phytologist, 215(2), 737-746).

Masters students:

Alexander Rose (2015, Masters student at Exeter; now a Graduate Teaching Associate at Bangor University)

Reinier van Velzen (2014, Visiting masters student at Exeter)

Amy McLeman (2013, Masters student at Exeter; now pursuing a PhD at the University of Exeter with Profs Richard Ffrench-Constant and Chris Bass to design bee-safe pesticides)

Jennifer Bates (2009, Masters student at Oxford)

Undergraduate researchers:

Fernando Trent Diaz: Fernando joined the Pear Project in 2019 to help isolate and characterize phages from the phyllosphere. He then received an NSF REPs fellowship to stay on the Pear Project and examine coexistence of strains within the phyllosphere.

Sophie Zhai: Sophie joined the lab in 2019 and worked with Cathy to understand the role of phylogeny in phage host range.

Ethan Kau: Ethan joined the lab in 2019, and worked with Wenke on understanding the role of the microbiome (and phages) in shaping disease.

Elodie Jungerman: Elodie joined the lab in 2019 and worked with Elijah in characterizing within-microbiome interactions using a synthetic phyllosphere community.

Nikita Chigullapally: Nikita joined the lab in 2019 and worked with Elijah in characterizing within-microbiome interactions using a synthetic phyllosphere community.

Joy He: Joy is a Nutritional Sciences – physiology major from Waterloo, Canada. She joined the lab in 2019 to work with Shirley Zhang on understanding the role of defensive symbionts in shaping disease outcome, and received a URAP Summer fellowship to examine the factors that shape pathogenesis.

Aspen Pastore: Aspen joined the lab in 2018 and is working on the interaction between phages and biofilm formation with Cathy Hernandez.

James Lu: James joined the lab in 2018 and worked with Elijah on variation in phage traits.

Rachel Rovinsky: Rachel joined the lab in 2017 and is working with Elijah on the role of bacterial and plant signaling molecules in inducing plant immunity.

Charmaine Fong: Charmaine joined the Pear project in 2018 to help track bacteria-phage dynamics in pear trees.

Kore Lum: Kore ran an experimental evolution project using two lytic phages that have evolved in a variety of environmental conditions with different strains of Pseudomonas syringae. She received a URAP summer research grant to complete this work.

Aditi Maheshwari: Aditi joined the lab in 2018 to work on the Pear project – helping us track the dynamics of bacteria and phages within the phyllosphere of diseased pear trees infected with Erwinina amylovora, the causal agent of fire blight disease.

Shirley Zhang: (2017-2020) Shirley joined the lab as a Sophomore working with Norma Morella on a project to determine the protective effects of bacterial communities against the pathogen P. syringae (Morella, N. M., Zhang, X., & Koskella, B. (2019). Tomato Seed-Associated Bacteria Confer Protection of Seedlings Against Foliar Disease Caused by Pseudomonas syringae. Phytobiomes Journal3(3), 177-190) She then completed her honor’s thesis exploring the coevolution between a pathogen and a protective symbiont, and is now a PhD student at Cornell!

Callie Cuff: Callie joined the lab in 2017 and worked with Britt on a project exploring natural bacteria-phage dynamics during fire blight infection of pear trees. She is now attending medical school at UCLA.

Michelle Leung: Michelle joined the lab in 2016 and was working with Britt, in collaboration with Jenn Lewis, on a method for rapidly identifying phage receptors allowing infection of the plant pathogen, P. syringae. She also collaborated on a large project exploring the impact of phages in the phyllosphere (Morella, N. M., Gomez, A. L., Wang, G., Leung, M. S., & Koskella, B. (2018). The impact of bacteriophages on phyllosphere bacterial abundance and composition. Molecular ecology27(8), 2025-2038). She is now attending Medical School at UCSF.

Shangyang Christopher Yang: Chris joined the lab in 2016 and worked with Norma on designing phage specific probes to measure phage-phage competition in vitro (Morella, N. M., Yang, S. C., Hernandez, C. A., & Koskella, B. (2018). Rapid quantification of bacteriophages and their bacterial hosts in vitro and in vivo using droplet digital PCR. Journal of virological methods259, 18-24). He is now attending Medical School at UCLA.

Nishani Abeydeera: (2015-2017, Volunteer, Berkeley) Nishani joined the lab within my first few months at UC Berkeley and worked here for nearly two years on projects ranging from phage genome sequencing to identifying new phage receptors on bacterial cells; now working as a medical scribe at the Northridge Hospital emergency room

Izaak Coleman: (2013, 2015, Volunteer, University of Exeter) now pursuing a PhD at Columbia University (see here).

Jennifer Weller: (2014, Undergraduate, University of Exeter) now doing a PhD at Queen’s University Belfast on aggression in domestic animals)

Benjamin Keningale: (2013, Undergraduate, University of Exeter) won Darwin award for top honor’s project in University of Exeter’s BioSciences department; just finished his MSc at the Royal Veterinary College and now deciding among PhD programs.

Olivia Lee: (2013, Undergraduate, University of Exeter) Graduatd with an MSc from University of Liverpool, then volunteered with Edze Westra, looking into the whens and whys of the evolution of CRISPR immune system in bacteria, and now a Lab technician at the University of Southampton, Clinical and Experimental Science department, looking into the effects of a novel topical pharmaceutical gel on skin cells cultured in vivo.

Derek Lin: (2010, Honor’s project student at UC Santa Cruz, where I was a postdoctoral fellow) now a research technician at the Biomedical Research Institute of New Mexico, and an active collaborator. He is interested in the role that phages play in the microbiome: Lin, D. M., Koskella, B., & Lin, H. C. (2017). Phage therapy: An alternative to antibiotics in the age of multi-drug resistance. World journal of gastrointestinal pharmacology and therapeutics8(3), 162.

Angela Pogson: (2015-2017, Volunteer, Berkeley) Angie joined us in her 1st year at Berkeley to work, in collaboration with Britt and Steve Lindow, on bacterial ice nucleation in the tomato leaf.

Priyanka Ranade: (2016-2018) Priyanka joined the lab in 2016 and was working with Cathy on bacteria-phage interactions within the leaves of tomato plants.

Grant Wang: (2016-2017, Volunteer, Berkeley) Grant spent over a year in the lab working closely with Norma to study the impact of phages within the tomato microbiome (Morella, N. M., Gomez, A. L., Wang, G., Leung, M. S., & Koskella, B. (2018). The impact of bacteriophages on phyllosphere bacterial abundance and composition. Molecular ecology27(8), 2025-2038); now beginning a 1-year’s masters program at Tufts University.

Visiting researchers:

Ana Luisa Soares de Vasconcelos (2019/2020): Ana was a visiting PhD student from the University of São Paulo, Brazil. She collaborated on a number of projects relating to how microbiomes adapt to the plant phyllosphere. See more about Ana and the fantastic work she is doing here: https://scholar.google.com.br/citations?user=P4k6wmcAAAAJ&hl=en

Nina De Luna (2019): Nina was an undergraduate at Pennsylvania State University who spent the summer working with Reena Debray on the loss of phage resistance due to fitness costs as an Amgen Scholar.

Rob Porch (2019): Rob was a visiting NSF REU scholar at Berkeley who is helping Kyle with his field study to examine the role of plant neighborhoods in the assembly of aboveground microbial communities.

Francis Weng (2018): Francis joined the lab for a semester at the end of his Phd on an Academia Sinica fellowship from the National Taiwan Normal University. He is working with us to apply network models to understand when and how a microbiome confers protection against a given pathogen.

Annika Gomez (2016): Annika is an undergraduate at Cornell University who spent a summer in the lab as part of the prestigious Amgen Scholars program.

William Feeney (2016): Will visited the lab for a summer as a Fulbright Fellow based between the University of Queensland (AUS) and the University of Delaware studying numerous coevolutionary interactions, including brood parasites. More here: http://www.williamefeeney.com

Stefanie Barbosa Potful Soares (2016): Stefanie is an undergraduate at the Federal University of Espirito Santo (UFES) in Brazil who worked in the lab over the summer as part of Brazil’s Scientific Mobility program.

Lab photo 2 May 2018

Lab group May 2018: Top row, from left: Tristan Caro, Shangyang Christopher Yang,  Rachel Rovinsky, Norma Morella, Elijah Mehlferber, Shirley Zhang, Britt Koskella; Bottom row, from left: Callie Cuff, Priyanka Ranade, Catherine Hernandez, Michelle Leung, and Alina Lee; Not pictured: Kore Lum.

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