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Day 3

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iFAST Microbial Ecology - Day 3

Computational Biology & Engagement

Date: Apr. 6, 2022

Time:  10:00 am - 12:30 pm U.S. EDT
            2:00 pm - 4:30 pm GMT
            10:00 pm - (Apr. 5) 12:30 am China

U.S. Eastern Daylight Time (EDT)

* The webinar will generally open 30 min earlier (9:30 EDT) for panelists and start broadcasting 10 min earlier (9:50 EDT).

10:00 am - 10:10 am


Janet Jansson is Chief Scientist for Biology and a Laboratory Fellow at the Pacific Northwest National Laboratory (PNNL) in Richland, Washington, USA. Jansson has more than 35 years of experience in microbial ecology. After obtaining her Ph.D. at Michigan State University (1988) she established a successful career in Sweden for 20 years and was Professor, Chair of Environmental Microbiology, and Vice Dean at the Swedish University of Agricultural Sciences prior to moving back to the United States in 2007. Jansson was a Senior Staff Scientist at Lawrence Berkeley National Laboratory from 2007-2014 and an Adjunct Professor at the University of California, Berkeley and at the University of Copenhagen, Denmark from 2012-2014. She moved to PNNL in 2014 and is currently focused on the impacts of climate change on the soil microbiome. Jansson is a Fellow of the American Academy of Microbiology, the Washington State Academy of Science, the American Association for the Advancement of Science and recipient of an Honorary Doctorate from the University of Helsinki, Finland. She has authored more than 250 publications and has been on the list of most highly cited researchers in the world for the past 4 out of 5 years. She is Past President of the International Society for Microbiology (ISME) and serves on numerous national and international advisory panels, including the National Academy of Sciences, U.S. National Committee for Soil Science, and the National Academy’s Decadal Survey for NASA.

10:10 am - 10:40 am

Keynote: When Push Comes to Shove: Scaling Microbial Processes

G. Philip (Phil) Robertson is University Distinguished Professor of Ecosystem Science in the Dept. of Plant, Soil and Microbial Sciences and the WK Kellogg Biological Station (KBS) at Michigan State University. He directs the USDA’s Long-term Agroecosystem Research (LTAR) site at KBS, has been science director for the DOE Great Lakes Bioenergy Research Center, and for 25 years directed NSF’s Long-Term Ecological Research (LTER) site at KBS. His research focuses on nitrogen and carbon dynamics, greenhouse gas fluxes, and land management solutions to climate change. He received his Ph.D. in Ecology and Evolutionary Biology in 1980 from Indiana University and his B.A. in 1976 from Hampshire College.

10:40 am - 10:55 am

Diving Deep into Microbial Genomic Data – Big Findings in Small Fungi, Bacteria, and Viruses

Patrick Chain is a Laboratory Research Fellow and a Senior Staff Scientist in the Biosciences Division at Los Alamos National Laboratory. Prior to LANL, he spent a decade at the Joint Genome Institute and at Lawrence Livermore National Laboratory leading various microbial genomics efforts. It was during his LLNL tenure that he met Jim Tiedje who both chaired a review panel for the Life Sciences Directorate at LLNL and was highly active with both DOE and the DOE JGI’s new programs exploring microbial genomics. Either due to shared love of microbiology, genomics or perhaps hockey, he was encouraged to enter a Ph.D. program at MSU, which was completed while working and throughout a transition between National Laboratories from LLNL to LANL. At LANL, his research currently includes investigating the breadth and nature of bacterial-fungal interactions using bioimaging and multi-omics, the development of algorithms for teasing apart taxonomy and functional signals in complex metagenomic and metatranscriptomic data, the implementation of standards for genomics and bioinformatics research, and the application of various genomics techniques and bioinformatics methods in the study of a broad range of environmental and animal-associated microbiomes.

10:55 am - 11:10 am

The Quest for What a Species Is: from the CME Time to Present

Dr. Kostas Konstantinidis is the Richard C. Tucker Professor in the School of Civil and Environmental Engineering and the School of Biological Sciences (adjunct) at Georgia Tech and Program Faculty for the Coulter Department of Biomedical Engineering at Georgia Tech and Emory University. He earned his BS (1999) in Agricultural Sciences from the Aristotle University of Thessaloniki, Greece and his PhD (2004) from the Center for Microbial Ecology at Michigan State University, under the supervision of James Tiedje. Prior to joining the faculty at Georgia Tech in 2007, he was a Postdoctoral Fellow in the Department of Civil and Environmental Engineering at MIT under the supervision of Ed DeLong. The overarching goal of his research is to advance understanding of how microorganisms adapt to human-induced environmental perturbations and to cause disease. He is also interested in biotechnological applications of microbial diversity in the bioremediation of environmental pollutants and the assessment of water quality. To achieve these goals, his lab has been developing novel culture-independent (e.g., metagenomics and metatranscriptomics) approaches and associated bioinformatics tools. Dr. Konstantinidis has published 170 papers in these areas, 13 in PNAS alone, which have received in excess of 21,500 citations (Google Scholar). Accordingly, he has made the top 1% of world's Highly Cited scientists and engineers list by Clarivate/Web of Science in 2020 and 2021, among several other distinctions and press releases. Further, his lab runs a bioinformatics server that makes the tools available for online analysis of microbial metagenome and genome data by external users; currently >3,000 users per month use this webserver.

11:10 am - 11:25 am

Unearthing Soil Viruses

Ruonan Wu is a computational scientist in the Biological Sciences Division at the Pacific Northwest National Laboratory in Richland, Washington. After receiving a bachelor’s degree at Hong Kong Baptist University in 2014, Ruonan started a 4-year PhD program (2014-2018) at the University of Hong Kong. During the last two years of her graduate study (2016-2018), Ruonan went to Michigan State University as a visiting student supervised by Dr. James Tiedje and Dr. James Cole. Ruonan then joined the Pacific Northwest National Laboratory as a postdoctoral researcher mentored by Janet Jansson (2018-2021). Her current research aims to discover cryptic viruses in soil environments and to understand their ecological impacts by integrating data obtained using multi-omics, molecular virology, and structural biology.

(5 min break)

11:30 am - 11:45 am

Science for Constructive Insurgency in Times of Climate Change

Arturo A. Massol-Deyá is from the mountainous area of Puerto Rico in the municipality of Adjuntas where his parents founded the community-based organization Casa Pueblo. Massol-Deyá grew up in this project and chairs its Board of Directors since 2007. A graduate of the public school system (1986) and the University of Puerto Rico (1990), he obtained his doctoral degree from the Center for Microbial Ecology at Michigan State University in 1994. Since then, he has been a faculty member at the Department of Biology of the University of Puerto Rico Mayagüez Campus where he established the Tropical Microbial Ecology Lab. He has been a mentor to numerous students and a principal investigator of projects on microbial ecology with emphasis on biological processes aimed at restoring contaminated environments. He is the author of multiple academic and opinion articles and has given numerous conferences nationally and internationally. Two recently published books Amores que luchan (2018) and Ciencia para la insurgencia (2020), and Energía y Democracia (In press) address the crises facing the country and from where it proposes that scientific knowledge and community engagement are key elements for social transformation.

11:45 am - 12:00 am

The Art of Microbiology: Community Building toward Environmental Problem Solving

Mary Beth Leigh is a professor of microbiology and coordinator of arts-humanities-STEMM integration at the University of Alaska Fairbanks. Her research interests include the biodegradation of contaminants in terrestrial, marine, and subsurface environments and biogeochemical cycling in high-latitude ecosystems. She is the founding director of a collaborative arts-humanities-science program called “In a Time of Change”, which is based within the Bonanza Creek Long-Term Ecological Research program in Alaska, and she helps to coordinate arts and humanities activities for the U.S. National Science Foundation’s Long-Term Ecological Research (LTER) Network. Prior to joining UAF in 2006, Leigh earned her B.F.A. in Modern Dance, M.S. in Botany, and Ph.D. in Microbiology all at the University of Oklahoma. From 2003-2006, she conducted postdoctoral research with Jim Tiedje at the Center for Microbial Ecology at Michigan State University and Mark Bailey at the U.K. Natural Environment Research Council’s Center for Ecology and Hydrology, Oxford. As a dancer and a cellist, she’s performed in stylistically diverse ensembles over the years, sometimes choreographing or composing pieces with a splash of science.


12:00 pm -  12:15 pm

Adina Howe is an associate professor of Agricultural and Biosystems Engineering at Iowa State University.  She leads the Genomics and Environmental Research in Microbial Systems (GERMS) Laboratory.  Her research focuses on understanding microbial interactions in agricultural and environmental systems to sustainably manage our land and water resources.  She earned a B.S. and M.S. in engineering at Purdue University and a PhD from the University of Iowa.  She was a postdoctoral research fellow at Michigan State University with Drs. C. Titus Brown and James Tiedje, followed by a position as a research scientist at Argonne National Laboratory.  Her research is supported by the USDA National Institute of Food and Agriculture; the National Science Foundation; the Environmental Protection Agency; and the U.S. Department of Energy, Office of Biological and Environmental Research.  She enjoys hiking with her family and two dogs, traveling, and food.

Website at Univ. Copenhagen

Kristian Koefoed Brandt currently leads the environmental microbiology research group at Department of Plant and Environmental Sciences, University of Copenhagen and is the head of the educational program Water and Environment at the Sino-Danish Center for Education and Research (SDC) in Beijing, China. Microbial ecotoxicology and ecology in agroecosystems and the environmental dimension of antibiotic resistance represent current research areas. He holds a PhD degree in microbial ecology (1998) from Aarhus University, Denmark. He has worked as a postdoctoral fellow (1998-2001) at the Royal Veterinary and Agricultural University (Denmark) and as a visiting scholar (2001-2002) at the Center for Microbial Ecology at Michigan State University (USA) and since then as an associate professor at KVL (2003-2006), University of Copenhagen (since 2007), and Sino-Danish Center (since 2013).

12:15 pm - 12:35 pm

Transitioning Through Time: me and ME

James Tiedje is University Distinguished Professor Emeritus of Microbiology and Molecular Genetics and of Plant, Soil and Microbial Sciences at Michigan State University, and was director of the Center for Microbial Ecology for 30 years. His contributions have been on microbial ecology, physiology and diversity, especially regarding the nitrogen cycle, biodegradation of pollutants and on the use of genomics and metagenomics to understand speciation, community structure and functions. He served as editor-in-chief of Applied and Environmental Microbiology and editor of Microbial and Molecular Biology Reviews and mBio. He served on the Board on Life Sciences of the National Research Council, EPA’s Science Advisory Panel and on DOE’s Biological and Environmental Research Advisory Committee. He was president of the American Society for Microbiology and the International Society of Microbial Ecology. He has received numerous awards, including UNESCO’s Carlos J. Finlay Prize in microbiology and ASM’s Applied and Environmental Research Award. He is a member of the U.S. National Academy of Sciences and the Chinese Academy of Sciences, and a Fellow of the AAAS, the American Academy of Microbiology, the Ecological Society of America, and the Soil Science Society of America.

Adjourning: Jizhong Zhou, University of Oklahoma