Current Lab Members

Mary Firestone, Professor of Environmental Science, Policy, and Management and Plant and Microbial Ecology 

Educational Background:

Ph.D. Soil Microbiology Michigan State University, 1979

Research Interests:

Soil microbial ecology: Microbial processing of carbon and nitrogen underlie the capacity of soil to support plant growth in agriculture, rangeland, forests, and wetlands. However the extreme heterogeneity of soil and the scale at which microorganisms interact with their habitat has made understanding the ecology of soil microbes a challenge of long duration. The research done in the Firestone lab aspires to fundamental understanding as well as knowledge applicable to current problems including terrestrial system response to global change, sustainability, biodegradation, and soil structure.

Honors and Awards:

  •    Fellow- American Geophysical Union 2016
  •    Betty and Isaac Barshad Chair in Soil Sciences 2016
  •    CNR Career Achievement Award 2013
  •    Berkeley Faculty Service Award 2011-12.  UC Berkeley Academic Senate.
  •    Senior Fulbright Fellow, Lincoln University,  New Zealand – Nov-Dec 2007.
  •    Eminent Ecologist in Residence, W.K. Kellogg Biological Station, MI, July 1997 & 2007.
  •    Clark Distinguished Lecturer, Soil Science Society Meetings, Seattle – 2004
  •    BBSRC Underwood Fellow, York University, UK 2004-05
  •    Brown & Williamson Distinguished Lecturer, University of Louisville – 2003
  •    Distinguished Environmental Scientist, Woods Hole – 2002
  •    Fellow – American Academy of Microbiology – 2002
  •    Distinguished Scientist, Institute for Ecosystem Studies,  N.Y. -1999
  •    Fellow – Soil Science Society of America – 1995

Staff

Katerina (Rina) Y. Estera-Molina, Staff Research Associate

Educational Background:

M.S. Rangeland Management, University of California, Berkeley

B.S. Microbial Biology University of California, Berkeley 2010

Research Interests:

Soil microbial ecology, root exudates, carbon cycling, rhizosphere

The main goal of my research is to contribute to a better understanding of how Mediterranean rangelands will respond to climate change. Mediterranean rangelands in California are an important source of forage production for livestock. Understanding the interactions among rangeland plants, soil and the soil microbial community is important in regards to soil health and the overall quality and quantity of forage production. My research focuses on the rhizosphere, the interface between the root and soil. Specifically, I am interested in the characterization of root exudates, compounds exuded by the roots. These exudates can act as a carbon source for the surrounding soil microbial community. Different types of exudates have the power to select for different types of microbial communities. This can in turn have an influence on the nutrient availability in the soil and other plants in the system. I will be working with Avena fatua, a wild oat commonly found in Mediterranean grasslands. I am investigating how the exudate composition changes over the lifetime of the plant, and if exudate composition will differ between plants grown in ambient verses elevated CO2 conditions. This characterization will help us achieve a better understanding of the potential response Mediterranean rangelands could have to climate change.

Sarah Baker, Staff Research Associate

Educational Background:

B.S. Biological Sciences, University of California, Irvine, 2010

Ph.D. Ecology and Evolutionary Biology, University of California, Irvine, 2016

Ilexis Chu-Jacoby, Staff Research Associate (Lab Manager)

Educational Background:

B.S. Molecular Environmental Biology, University of California, Berkeley, 2017

Awards:

Ronald E. McNair Scholars Program; Sponsored Projects for Undergraduate Research

Senior thesis title: Assessing Persistence of Soil Carbon Mineral Bonds in the Presence of Iron and Aluminum

Research Interests:

soil geochemistry, environmental chemistry, carbon cycling, climate change, soil microbial ecology

My research investigates how a complex soil environment influences chemical bonds between soil organic carbon and mineral surfaces. I am interested in the ecosystem and biogeochemical properties that influence carbon cycling through soil: the plants depositing fixed carbon into the soil; the microbes which respire organic carbon back to the atmosphere; and the minerals that protect carbon from microbial degradation, enabling mineral-associated organic carbon to persist in soil for thousands of years. My research more specifically characterizes these persisting carbon-mineral bonds, tracing the origin of the mineral-associated carbon with stable isotopes. Through chemical extractions, I measure the strength of soil carbon-mineral bonds to elucidate the fundamental mechanisms by which organic carbon persists in soil.
Continuing work in the Firestone Lab provides me the opportunity to engage with further knowledge and techniques in microbiology, density fractionation, and various chemical analytics with mass spectrometry.

Alyssa Byer, Lab Technician

Aaron Chew, Lab Technician

Post-Doctoral Students

Nameer R. Baker

E-mail: nameer@berkeley.edu

Twitter: @nameerbaker

Educational Background:

B.Sc.H University of Kansas, Ecology and Evolutionary Biology, 2011

B.A.H University of Kansas, Anthropology, 2011

Ph.D. University of California, Irvine, Ecology and Evolutionary Biology, 2016

Research Interests:

Soil microbial ecology, nutrient cycling, anthropogenic change

During my postdoc I will be working on a collaborative DOE project seeking to understand how interactions between switchgrass and microbial communities in the rhizosphere aid establishment and growth of switchgrass in marginal agricultural soils. For my Ph.D., I investigated how aspects of climate and future climate change in southern California may affect carbon-cycling processes in litter, with a focus on the activity and efficacy of extracellular enzymes produced by microbial decomposer communities.

Publications:

Baker, N.R. & Allison, S.D. (2015) Ultraviolet photodegradation facilitates microbial litter decomposition in a Mediterranean climate. Ecology, 96(7):1994-2003. doi:10.1890/14-1482.1

Mengting (Maggie) Yuan

B.E. Environmental Engineering, Tsinghua University, 2011

Ph.D. Microbiology, University of Oklahoma, 2017

Awards:

Institute for Environmental Genomics (IEG) Excellent Student Award, 2017

George L. and Cleo Cross Graduate Student Endowed Scholarship, University of Oklahoma, 2016

American Society of Microbiology Student Travel Grant, 2014

Research Interests:

Soil microbial ecology, terrestrial nutrient cycle, rhizosphere biology, climate change

My research aims at contributing to a clearer picture of the paths and fates of photosynthetic carbon, and how climate change affects them, by studying belowground biotic and abiotic processes, especially at rhizosphere, the interface of root and soil. For my post-doc, I will be working on a collaborative project addressing 1) the controlling of belowground carbon dynamics through multi-trophic interactions of plant, bacteria, archaea, fungi, soil fauna, and phage; 2) the effect of decreased precipitation on these processes in a Mediterranean grassland ecosystem. For my Ph.D., I studied the responses of soil microbial community composition, functional potential, and microbe-related soil processes to climate warming in both a temperate tall grassland ecosystem and at a high-latitude tundra underlain with permafrost.

Publications:

Google Scholar: https://scholar.google.com/citations?user=RvUbaacAAAAJ&hl=en

Research Gate: https://www.researchgate.net/profile/Mengting_Yuan

Ella Sieradzki

B.Sc. Tel Aviv University, Biology, 2007

M.Sc. Tel Aviv University, Ecology and Environmental Studies, 2009

Ph.D. University of Southern California, Marine Biology and Biological Oceanography, 2017

Awards:

Provost Ph.D. fellowship, 2012

Norma and Jerol Sonosky Environmental sustainability graduate summer fellowship, 2014, 2015

Research interests:

Soil microbial ecology, carbon cycling, soil viruses

I am generally interested in the interplay between microbes and their environment. As a post doc co-advised by Mary Firestone and Jill Banfield I’ll be focusing on carbon flow from plants into soil bacteria and archaea and eventually viruses using stable isotope probing and metagenomics. During my PhD I used stable isotope probing to study incorporation of carbon from naphthalene in marine bacteria, as well as prevalence of various light harvesting mechanisms and active viral infections using metagenomics and metatranscriptomics.

Publications:

Research Gate: https://www.researchgate.net/profile/Ella_Sieradzki

Alex Greenlon

E-mail: agreenlon@berkeley.edu

Educational Background:

B.A.: Molecular, Cellular, and Developmental Biology; University of Colorado, Boulder

Ph.D.: Plant Pathology; University of California, Davis, 2018

Awards:

USAID Borlaug Fellow, 2015

Research Interests:

Soil organic carbon stabilization, Soil microbial ecology, Metagenomics, Microbial biogeography, Legume-Rhizobium symbiosis, Nitrogen fixation

As a postdoc in the Firestone and Banfield labs, I am applying metagenomics and quantitative stable-isotope probing (qSIP) to understand how plant-derived carbon moves through soil microbial communities, and what factors (soil type, moisture, season) affect the outcome of this cycle (whether this carbon respires back into the atmosphere or stabilizes as soil-organic matter). For my PhD I studied the global genomic diversity of the nitrogen-fixing bacterial symbionts of the legume crop chickpea.

Publications:

Google Scholar

Graduate Students

Rachel Neurath

Educational Goal:

PhD in Environmental Science, Policy, and Management

Educational Background:

B.A. Smith College, Earth and Environmental Science, 2009

M.S. Dartmouth College, Earth Sciences, 2011

Research Interests:

Soil microbial ecology, carbon cycling, soil geochemistry

My research focuses on the interactions between plants, microorganisms, and soil minerals that control carbon stabilization in soil. Plants are the primary source of carbon to soils, while soil microbes are the central transformers, metabolizing carbon substrates for energy and growth. While a significant portion of carbon that enters the soil reservoir is quickly respired back to the atmosphere, some of that carbon persists for up to thousands of years. The oldest carbon in soils is associated with soil minerals, which physically and chemically protect carbon from microbial degradation. In my research, I examine the processes that control what carbon substrates associate with different mineral types, and how long they remain associated with those minerals. The central focus of my work is the role of soil microorganisms in these processes of mineral association and dissociation – both as consumers and transformers of soil carbon, but also as a part of the soil carbon pool themselves.

Heejung Cho

Educational Goal:

PhD in Plant and Microbial Biology

Educational background: B. A. Yonsei University, Systems Biology, 2013

Research interests: soil microbial ecology, evolution, genomics

My research focuses on the role of microbial traits on their ecology and evolution in soil. Soil is one of the most complex habitats for microbes on Earth; biotic factors such as microbe-microbe interactions, plant-microbe interactions and abiotic environmental factors influence the fitness and evolution of life in soil. In many soil habitats such as Californian semiarid grassland soil, plant roots drive dynamic environmental changes in soil. As plant roots grow through soil, bacteria living in the rhizosphere experience environmental shifts. Changing environment selects soil bacteria based on their traits. My current project focuses on studying bacterial traits and genomic features that promote their growth in rhizosphere. Using Californian grassland rhizosphere succession as my first model, I wish to better understand the role of microbial traits on their life in varying environment.

Anne Kakouridis

Educational Goal:

Ph.D. in Environmental Science, Policy, and Management

Educational Background:

B.S. University of Utah, Biology, 2011

M.A. Harvard University, Organismic and Evolutionary Biology, 2014

Research Interests

Fungi, plant-microbe interactions, symbiosis, carbon cycling, climate change

My research focuses on the role of soil fungi in the carbon cycle and their potential to mitigate climate change by increasing carbon sequestration. Of the estimated 5 million species of fungi, many play crucial roles in ecosystems. In particular, soil fungi are involved in the carbon cycle as decomposers and plant symbionts, but the magnitude of their importance in soil carbon storage in unclear.  The main focus of my work is to assess the role of arbuscular mycorrhizal fungi in the carbon flow from roots to the rhizosphere and ultimately to stabilized carbon in soil organic matter. My goal is also to determine how climate change affects fungal communities by identifying and quantifying arbuscular mycorrhizal fungi under current and predicted future climatic conditions.

Alexa Nicolas

Educational Goal:

Ph.D. in Plant & Molecular Biology

Educational Background:

B.A. Molecular Biology, University of Pennsylvania

Awards:

NSF Graduate Research Fellow, Honorable Mention

Intel Science Talent Search Semifinalist (now Regeneron STS, formerly Westinghouse)

Research Interests:

Soil microbial ecology, viral ecology, nutrient sharing, vitamin biosynthesis

Our soils hold one of the largest carbon reserves on the planet. Microbes are central to soils’ carbon sequestration capacity. Soils are complicated environments where microbes live among different-sized particles, water and air, and nutrients. How do these soil microbes live together in communities and share resources? When microbes die their desirable contents spill into the local environment and become publicly available to neighbors. However, how microbes die is difficult to pinpoint, especially in complex environments like soil. Viruses, an understudied member of microbial communities, can kill microbes. Understanding the dynamics of viruses in soil provides a deeper understanding into how communities form, and potentially, build cooperative
networks.

Before pursuing a PhD, Alexa worked as an educator at a science museum, as an editor at a major academic journal company, as a writer at a stem cell research non profit, and as an evaluator at a restoration ecology NSF-funded grant reintroducing oysters into the New York harbor. Outside the lab, Alexa experiments with soil in a soil-based artistic practice.

Christina Fossum, M.S. Student

Undergraduate Students

Cynthia-Jeanette Mancilla

Emily Kline

Madeline Moore

Melanie Rodriguez

Laura Adame

Tasnim Ahmed

David Sanchez