Simons Early Career Investigator in Marine Microbial Ecology and Evolution Awards

Important Dates
  • LOI Available
  • Reference Letters Deadline
  • LOI Deadline
  • LOI Notification
  • Full Proposal Deadline (Finalists Only)
  • Award Notification
  • Award Start Date
Contact Info

Simons Early Career Investigator in Marine Microbial Ecology and Evolution Awards 2018 Request for Applications

The Simons Foundation is now accepting applications for its Simons Early Career Investigator in Marine Microbial Ecology and Evolution Awards. The deadline for receipt of letters of intent (LOI) is November 6, 2017, 5:00 PM Eastern Standard Time.


Microbes inhabit and sustain all habitats on Earth. In the oceans, microbes capture solar energy, catalyze biogeochemical transformations of important elements, produce and consume greenhouse gases, and provide the base of the food web.

The purpose of these awards is to help launch the careers of outstanding investigators who will advance our understanding of marine microbial ecology and evolution through experiments, modeling or theory. Projects focusing on the microbiomes of invertebrates or vertebrates or on paleontological records will not be considered this year. Investigators with backgrounds in different fields are encouraged to apply.


Applicants must hold a Ph.D. or equivalent degree. She/he must have carried out research in a tenure-track or equivalent independent position for at least one year and no more than eight years (start date between November 2009 and November 2016) and must currently hold a tenure-track, tenured, or equivalent independent position in a U.S. or Canadian institution. She/he must be the principal investigator (PI) or co-PI currently or within the past year on a research grant from a national governmental agency or major foundation.

About the Awards

Grants will be for $180,000 USD per year, including indirect costs (limited to 20 percent of modified total direct costs), for a period of three years, subject to annual reviews and continuation of research in areas relevant to the purpose of this program. Appropriate expenses include salary support for the investigator and postdoctoral and graduate research assistants, travel, equipment, supplies and other research expenses. Awards will begin April 1, 2018. Awards will be governed by the Simons Foundation policies, which can be found at

Submission of Letter of Intent

Prospective applicants must submit a letter of intent (LOI) by November 6, 2017, 5:00 PM Eastern Standard Time. LOIs must be completed electronically and submitted using forms provided at Please log in as an applicant, go to the grant opportunities tab, scroll to simons foundation and click apply now for the “Simons Early Career Investigator in Marine Microbial Ecology and Evolution Awards” program. For assistance, please call 800-875-2562 or email

The following templates must be downloaded and submitted to proposalCENTRAL:

  1. Biosketch of investigator, including the start date of first appointment in an independent position, complete publications list, and past, current and pending support (two-page limit, excluding support).
  2. Narrative describing your research vision and plan (two-page limit, excluding references and up to three figures).
  3. Paragraph describing the significance of your most important publication during the last five years and your contribution to the work reported in the paper (250 words).
  4. Two letters of recommendation from former mentors or other scientists who are familiar with your research. Confidential letters must be submitted through proposalCENTRAL (see instructions available for download in proposalCENTRAL) by October 30, 2017, 5:00 PM Eastern Daylight Time.

Review Process

The review process will include evaluations by experts in the field, who will make recommendations to the Simons Foundation Life Sciences staff. LOIs selected for further consideration will be announced by February 1, 2018.

Full applications will require submission of a budget and brief budget justification, renewable reagents and data-sharing plan, and signature page with institutional approval by February 22, 2018. Applicants will be notified of decisions by March 15, 2018. The foundation anticipates appointing up to four investigators in 2018.


Administrative inquiries: | 646-751-1280
Technical assistance: | 800-875-2562

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Important Dates
  • LOI Available
  • Reference Letters Deadline
  • LOI Deadline
  • LOI Notification
  • Full Proposal Deadline (Finalists Only)
  • Award Notification
  • Award Start Date
Contact Info


The submission deadline for LOIs is Monday, November 6, 2017, 5:00 PM Eastern Standard Time. Please plan carefully with your host institution and references to meet this deadline. No extensions will be given.

proposalCENTRAL Log-In Information

New users first need to create a user account on proposalCENTRAL (pC) at To create a new account, go to (pC) and click CREATE ONE NOW under APPLICATION LOGIN. Fill in the required fields, check the boxes to agree to pC’s Terms of Service and Acceptable Use Policy and then click SAVE. For all users with a pC account, log in under APPLICATION LOGIN at and select CREATE NEW PROPOSAL or click on the GRANT OPPORTUNITIES tab. Scroll down to SIMONS FOUNDATION and then click APPLY NOW for the “Simons Early Career Investigator in Marine Microbial Ecology and Evolution Awards” program in order to start the LOI and access the templates. After all sections are completed, you will be able to click on the SUBMIT button to send.

To submit a LOI, the following proposalCENTRAL modules must be completed:

  1. Title Page
    1. Enter your project title in this section.
  2. Download Templates & Instructions
    1. All templates necessary to complete your LOI are available for download in this module (or the LOI ATTACHMENTS module, where attachments are submitted as PDF-only files; see the LOI Attachments section below for more details).
  3. Enable Other Users to Access This Proposal
    1. This module allows you to give other users access to your LOI. When you give a person access to your LOI, you can give them one of three levels of permissions: View, Edit or Administrator.
  4. Applicant/PI
    1. Enter the name of the principal investigator (PI) for the proposed funding here. While the PI does not need to submit the LOI him/herself, this section must be completed for the intended PI for proper proposal tracking and review.
  5. Organization/Institution
    1. Institution information is preloaded from the institutional profile but may be changed on this screen if necessary.
  6. Letters of Recommendation (Note: deadline is Monday, October 30, 2017.)
    1. Two confidential letters of recommendation from former mentors or other scientists who are familiar with your research are required with LOI submission.
    2. In this section, you will be able to list the references who will submit letters of recommendation on your behalf through our confidential submission process. To enter the references:
      1. Enter and confirm the email address of the reference you have chosen in the text box provided and click the add.
      2. A small pop-up window will open, prompting you for the reference’s first and last name. If the reference is already registered in proposalCENTRAL, the name will automatically display in the window.
      3. Enter the reference’s full name and click send email and then close window.
    3. An email will be sent to the reference from proposalCENTRAL requesting a confidential letter of recommendation. The email will include instructions, the reference’s proposalCENTRAL account information and a link for the reference to upload the completed letter of recommendation directly to your grant application. To ensure confidentiality, you will not have access to these letters. Once the email is sent, the reference’s name and contact information will appear under the LETTERS OF RECOMMENDATIONS section in your LOI. The referee information is displayed in the table: name, email address, date/time email was sent, etc. You can refer to this table to check on the status of the letters that have been uploaded to your LOI. When each of the letters is uploaded, the status will display as SUBMITTED.
    4. Repeat this process for each referee you wish to add. You will not be able to submit your proposal until two references are uploaded. Please plan accordingly with your references. No extensions will be given.
    5. The deadline for your references to submit the letters of recommendation is Monday, October 30, 2017, 5:00 PM Eastern Daylight Time. You will not be able to submit your application if both letters of recommendation are not submitted.

NOTE:  References will not have access to any portion of your LOI in the upload process.

  1. LOI Attachments
    1. The following documents are to be uploaded in this section, where the templates are also available for download:
      1. LOI Narrative: Upload a narrative in PDF format describing your research vision and plan (two-page limit, excluding references and up to three figures). Please note that LOI Narratives exceeding the limit of two pages will not be reviewed.
      2. Description of Publication: Upload a paragraph in PDF format describing the significance of your most important publication during the last five years and your contribution to the work reported in the paper (250 words).
      3. PI Biosketch: Upload a biosketch of the investigator in PDF format, including the start date of first appointment in an independent position, complete publications list, and past, current and pending support (two-page limit, excluding support).
  2. Validate
    1. You must click the VALIDATE button on the bottom of the page to check for any missing information or files that are required to submit the LOI. All missing information that is required will be listed on the screen. Please correct any missing information before proceeding to the next step.
  3. Submit
    1. You will be unable to submit if you have not provided all the required information. Any missing information will be listed on the screen. If your submission is successful, you will receive a confirmation message on the screen and a confirmation email.


Program inquiries:  
Administrative inquiries: | 646-751-1280
Technical Assistance:  | 800-875-2562


Important Dates
  • LOI Available
  • Reference Letters Deadline
  • LOI Deadline
  • LOI Notification
  • Full Proposal Deadline (Finalists Only)
  • Award Notification
  • Award Start Date
Contact Info
  1. Where do I submit the LOI?plus--large

    New users first need to create a user account on proposalCENTRAL (pC) at (For instructions on how to create an account, see the FAQ How do I create a proposalCENTRAL user account? below.) For all users with a pC account, log in under APPLICATION LOGIN at and select create new proposal or click on the GRANT OPPORTUNITIES tab. Scroll down to SIMONS FOUNDATION and then click APPLY NOW for the “Simons Early Career Investigator in Marine Microbial Ecology and Evolution Awards” program in order to start the LOI and access the templates. After all sections are completed, you will be able to click on the SUBMIT button to send.

    With an accepted LOI, you then gain access to the full proposal application on proposalCENTRAL. (For more information on submitting a full proposal, see Full Proposal FAQs below.)

  2. How do I create a proposalCENTRAL user account?plus--large

    Go to (pC) and click CREATE ONE NOW under APPLICATION LOGIN. Fill in the required fields, check the boxes to agree to pC’s “Terms of Service” and “Acceptable Use Policy” and then click SAVE.

  3. Can I email or mail an LOI?plus--large

    No, the Simons Foundation only accepts LOIs submitted online through

  4. Do I need an institutional sign-off to submit an LOI?plus--large

    No, however, successful finalists will need an institutional sign-off for the full proposal.

  5. Can someone else (assistant, staff member, etc.) submit my application for me?plus--large

    Yes, you can add users with administrator access to the pC application so that someone other than the Principal Investigator (PI) can edit and submit the application. To add another user, go to section 3, “Enable Other Users to Access This Proposal,” and complete the required fields.

  6. Can postdoctoral associates apply as Principal Investigators?plus--large

    No, postdoctoral associates may not apply as PIs. All applicants and key collaborators must hold a Ph.D., M.D. or equivalent degree and have a faculty position or the equivalent at a college, university, medical school or other research facility. Funds may not be used for stipend supplementation unless specifically authorized under the terms of the program from which the funds are derived.

  7. Can foreign institutions apply for this grant?plus--large

    Applicants must currently hold a tenure-track or tenured position or equivalent at a U.S. or Canadian institution.

  8. Can multiple Principal Investigators apply for a grant?plus--large

    No, we are not accepting applications with multiple PIs for this program.

  9. I will have one or more collaborators on my proposal. May I include multiple PIs or other senior personnel on my budget?plus--large

    No. You may provide funds for others to work on your research or educational activities, but they may not be listed as multiple PIs or in the senior personnel section of the proposal, within the primary budget or within a sub-award to a collaborating institution. However, you may pay someone as a consultant in your project or pay for his or her travel and field/lab expenses, materials and supplies, or access fee to a laboratory.

  10. Can I change the named Principal Investigator?plus--large

    Yes, linked instructions for how to change the named PI can be found in the application.

    The person who starts an application will be named as the PI on the Applicant/PI page. If the Applicant/PI section does not show the correct person (e.g., someone else started the online application and you are the PI, or you started the application and someone else is the PI), then you must update this section before submitting. PI details carry over to the full proposal.

  11. Can Principal Investigators submit multiple applications to this program?plus--large

    No, PIs cannot submit multiple applications to this program.

  12. What are the file format, font style and size requirements of the LOI?plus--large

    Please submit a PDF of the LOI document. Type should be set in 11-point, legible font. All margins should be set at 0.5 inches.

  13. Do I need to submit biosketches with the LOI?plus--large

    Yes. A biosketch is required for the Principal Investigator only.

  14. Can I submit a budget with the LOI?plus--large

    No, a detailed budget is not requested with the LOI.

  15. Where is the SUBMIT button?plus--large

    The SUBMIT button is located in the last section of the LOI. You will be unable to submit if you have not provided all the required information. If the submission deadline has not passed, use the validate button to check for missing requirements. If the problem persists, please contact

    If the deadline has passed, the submission period has closed and you will not be able to submit.

  16. I get an error message citing a missing section when I try to submit the LOI?plus--large

    The VALIDATE button reviews your LOI for missing sections. The submission instructions list the required sections and attachments. You must complete the missing sections listed. If you are still receiving error messages after completing and saving the indicated sections, please contact

  17. Are deadline times adjusted for time zones?plus--large

    No, please be advised that deadlines are in Eastern Time. We recommend registering early and submitting LOIs with ample time for corrections prior to the deadline hour. Site traffic can slow page-load times. The SUBMIT button will not work after the deadline time has passed.

  18. Is there a confirmation email when I submit the LOI?plus--large

    A confirmation email is sent upon submission of the LOI. Please contact if you submitted your LOI and have not received a confirmation email within 10 minutes. Make sure that spam filters allow emails from The LOI will be in the SUBMITTED tab when you next log in.

  19. Can I make changes to the LOI once it has been submitted?plus--large

    Before you can make changes to your submitted LOI, you must first contact the Simons Foundation. Please email or call (646) 751-1280. LOIs can only be changed prior to the November 6, 2017, deadline.

  20. Does the Simons Foundation grant extensions for LOIs?plus--large

    No extensions will be given. If you have any difficulties, please email or call (646) 751-1280. Please do not contact directly.

  21. How do I submit a full proposal?plus--large

    With an accepted LOI, you gain access to the full proposal application on proposalCENTRAL. Log in under APPLICATION LOGIN at, select the MANAGE PROPOSALS tab and then click in PROGRESS. Click the EDIT button for the corresponding application you want to complete. Once all sections are complete and the attachments are uploaded, the SUBMIT button will be activated and you can click SUBMIT to send your application.

  22. What are the font style and size requirements of the proposal?plus--large

    Type should be set in 11-point, legible font. All margins should be set at 0.5 inches.

  23. Is there a minimum percent effort for Principal Investigators?plus--large

    We seek applications from independent investigators who can devote a substantial portion of time to this project. While we do not require a minimum Principal Investigator (PI) effort, we expect the PI to commit to a level of effort that reflects a leading role in the project.

  24. Are indirect costs included in the annual budget limits?plus--large

    Yes. For example, the annual limit for an award is $180,000, which includes indirect costs at 20 percent. Please note that indirect costs cannot be taken on equipment with a unit cost of more than $10,000 or on tuition.

  25. Does the Principal Investigator need to sign the signature page?plus--large

    No, only the signing official is required to sign the signature page.

  26. Is there a confirmation email when I submit the proposal?plus--large

    A confirmation email is sent upon submission of the full proposal. Please contact if you submitted your full proposal and have not received a confirmation email within 10 minutes. Make sure that spam filters allow emails from The full proposal will be in the SUBMITTED tab when you next log in.

  27. I get an error message citing a missing section when I try to submit the proposal?plus--large

    The VALIDATE button reviews your full proposal for missing sections. The submission instructions list the required sections and attachments. You must complete the missing sections listed. If you are still receiving error messages after completing and saving the indicated sections, please contact

  28. Can I make changes to the application once it has been submitted?plus--large

    Before you can make changes to your submitted application, you must first contact the Simons Foundation. Please email or call (646) 751-1280. Applications can only be changed prior to the February 22, 2018, deadline.

  29. Is validating my proposal the same as submitting it?plus--large

    No. Validating the full proposal checks for errors and omissions and will alert you to missing requirements of your full proposal. If the full proposal is complete, you must then click SUBMIT. You will receive an email within 10 minutes. Contact if you do not receive confirmation and do not see your full proposal in the SUBMITTED tab or with the status changed to SUBMITTED.

  30. The deadline for notification has passed. What is the status of my proposal?plus--large

    You should receive notification within 24 hours of the deadline. Please check your spam filter settings if you have not received notification by then.

Andrew Barton, Ph.D.

Scripps Research Institute

Andrew Barton is an Assistant Professor at the Scripps Institution of Oceanography and at the section of Ecology, Behavior and Evolution of the University of California, San Diego. His research combines observational and numerical modeling perspectives to understand the fundamental mechanisms that regulate microbial population dynamics, community structure, biogeography and biodiversity in the ocean. Barton investigates how changes in Earth’s climate, including natural variability and long-term changes driven by human activities, have the potential to alter microbial species distributions and community composition through time. He received a B.A. in Science of Earth Systems from Cornell University (2000) and a Ph.D. in Climate Physics and Chemistry from Massachusetts Institute of Technology (2011). He was an NSF International Research Postdoctoral Fellow hosted jointly between Duke University and the University of Liverpool in the United Kingdom, and later was an Associate Research Scholar at the Geophysical Fluid Dynamics Laboratory at Princeton University.
Project: Environmental and ecological drivers of marine microbial morphology
The diversity of photosynthetic marine microbes can be astonishingly high, with up to hundreds of species coexisting in a single teacup of seawater. The coexisting community exhibits tremendous variation in cell size, shape and coloniality (some species form chains of cells, for example), and this morphological variation may help sustain species diversity by providing multiple avenues for species to survive in the ocean. Far from being ecological curiosities, morphological variations impact ecosystem function by influencing the export of carbon from the ocean surface to greater depths. To date, however, we have limited understanding of what sustains this great morphological variation and its wider significance.
The proposed work is an interdisciplinary and multi-methodological research campaign to study the environmental and ecological drivers of the size and shape of phytoplankton cells and colonies. We will use high-resolution underwater images of phytoplankton cells, colonies and zooplankton from the Scripps Plankton Camera (, in combination with oceanographic and atmospheric observations, to quantify how the size, shape and aspect ratio of phytoplankton cells and colonies vary with environmental and predatory conditions. We will complement the observational program by developing novel trait-based numerical models of the plankton community that resolve varying body size, form and colony size. Our aim is to extend the lessons learned at Scripps Pier to the globe using coupled ocean circulation, biogeochemical and plankton community models, where we can quantify biogeographic patterns of morphology and their biogeochemical impacts. Thus, the goals of the proposed research are to: a) understand how environmental and ecological processes shape phytoplankton and colony morphology and b) map and predict the diversity and biogeography of morphologies over the global ocean and their significance.

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Erin Bertrand, Ph.D.

Dalhousie University

Erin Bertrand is an Assistant Professor and NSERC Tier II Canada Research Chair in Marine Microbial Proteomics in the Biology Department at Dalhousie University, Halifax, Nova Scotia. Erin received a B.S. with honors in Chemistry and Environmental Studies from Bates College in 2005. She went on to complete her Ph.D. in Chemical Oceanography in the MIT/WHOI Joint Program, where she was awarded the Fye Award for Excellence in Chemical Oceanography research, 2010–2015. From 2012 to 2015, Erin was a U.S. National Science Foundation Office of Polar Programs Postdoctoral Fellow at the J. Craig Venter Institute and Scripps Institution of Oceanography. Her research aims are focused on understanding how microbes influence ocean biogeochemistry. She is particularly interested in the molecular basis of microbial micronutritional requirements and what the consequences of those requirements are for global carbon, nitrogen and sulfur cycling. Her group employs a range of quantitative mass spectrometry–based techniques, paired with field and laboratory experiments, to ask these questions.
Project: Quantifying the impact of rising temperatures on microbial micronutrient demand
Marine primary productivity, conducted largely by phytoplankton, forms the base of marine food webs and is a major factor in determining the relationship between the ocean and atmospheric CO2 concentrations. Temperature, nutrient and light availability are key drivers of phytoplankton growth. Questions regarding how these variables interactively influence photosynthetic microbes remain and are a major source of uncertainty in efforts to predict future changes in marine primary productivity. Along with macronutrients like nitrogen, phosphorus, and silica, phytoplankton also require a suite of micronutrients including iron, zinc, and cobalamin (vitamin B12). In vast regions of the surface ocean, phytoplankton growth is limited by the availability of these micronutrients. Given the extent of this limitation as well as the fact that micronutrient availability is projected to change regionally in the coming decades, understanding the ramifications of simultaneous alterations in micronutrient availability and temperature for phytoplankton growth is imperative. Available evidence suggests that micronutrient demand may decrease in the face of elevated temperatures; however predictions from cellular models are not always reflected in observations and so major uncertainties remain. This research program aims to identify, quantify and contextualize interactions between micronutrient demand and temperature in marine microbes. This research program will use a combination of quantitative field, laboratory and metabolic modeling approaches to (1) enhance our understanding of the role of micronutrients in a changing ocean, (2) offer empirical data for evaluating fundamental questions about the relationships between matter and energy balance in microbial ecology, and (3) provide clarity to global modeling efforts seeking to predict changes to primary productivity in the future ocean.

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Anne Dekas, Ph.D.

Stanford University

Anne Dekas is an Assistant Professor at Stanford University in the Earth System Science Department, studying the microbiology and biogeochemistry of the deep sea. She is broadly interested in how microbial life affects the chemistry and climate of the planet, today and throughout time. Her research combines tools from molecular biology and isotope geochemistry to identify and quantify microbial metabolic capabilities, activity and interactions, with a focus on understanding uncultured microorganisms in deep-sea water and sediment. Before joining the faculty at Stanford, she was a Lawrence Postdoctoral Fellow at Lawrence Livermore National Laboratory in the Chemical Sciences Division, where she investigated the carbon metabolic flexibility of pelagic marine archaea. She received a Ph.D. in Geobiology from the California Institute of Technology for her research on nitrogen fixation, methane oxidation and sulfate reduction at deep-sea methane seeps. She received an A.B. in Earth and Planetary Sciences from Harvard University on the Biogeochemistry track. Originally interested in space sciences, Dekas performed research at three NASA centers (Jet Propulsion Laboratory, Ames Research Center and Goddard Space Flight Center) before beginning her Ph.D., and she continues to be interested in the survival strategies of life in extreme environments.
Project: Quantifying microbial activity in the deep sea using NanoSIMS
The deep sea, also known as the dark ocean, is one of the largest habitats for microbial life on the planet: it covers nearly two thirds of the Earth’s surface and harbors approximately 55 percent of all marine microorganisms. Although severely understudied relative to the photic zone, the activity of deep microbial life plays an important role in marine biogeochemical cycling. In particular, recent evidence has shown the importance of chemoautotrophic Thaumarchaea, a phylum of archaea comprising about 20 percent of all marine microbes, in the cycling of nitrous oxide and carbon dioxide, both greenhouse gases. Our knowledge of the diversity and distribution of microorganisms in the deep sea has expanded in recent years with the development of next generation sequencing (i.e., “-omics”) methodologies. However, our understanding of microbial activity in the deep sea, including its phylogenetic and physicochemical controls, is still lacking. Closing this gap in our knowledge will increase our understanding of greenhouse gas cycling in the marine environment, and will better equip us to predict the activity of deep-sea microorganisms in a changing climate. This project will develop and utilize new methods to use nanoscale secondary ion mass spectrometry (NanoSIMS) — a tool to measure the isotopic composition of individual, uncultured cells — to quantify and characterize microbial activity in deep ocean waters. Combined with metagenomic and metatranscriptomic analyses, this work will link geochemical and molecular datasets, and specifically address the role of Thaumarchaea in deep-sea biogeochemical cycling.

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Naomi M. Levine, Ph.D.

University of Southern California

Naomi Levine is a Gabilan Assistant Professor of Biological Sciences and Earth Sciences at the University of Southern California. She received her B.A. in Geosciences from Princeton University and her Ph.D. in Chemical Oceanography from the MIT-WHOI Joint Program. Naomi’s interest in the interactions between fluctuating environments and ecosystem dynamics led her to join Paul Moorcroft’s lab at Harvard University as a NOAA Climate and Global Change Postdoctoral Fellow. In 2013, Naomi joined the faculty at USC, where she holds joint appointments in Marine and Environmental Biology, Molecular and Computational Biology, and Earth Sciences. Her research focuses on understanding the interactions between climate and marine microbial ecosystem composition and function. The Levine lab is developing novel modeling approaches that explicitly represent the response of dynamic microbial communities to a variable and changing environment. Naomi is the recipient of an Alfred P. Sloan Foundation Research Fellowship in Ocean Sciences.
Project: The role of marine microbial plasticity in evolution and biogeochemistry
Marine microbes are the engines of global biogeochemical cycling in the oceans. They are responsible for approximately half of all photosynthesis on the planet and drive the ‘biological pump,’ which transfers organic carbon from the surface to the deep ocean. Therefore, it is important to determine how marine microbes will adapt and evolve to a changing climate in order to understand and predict how the global carbon cycle may change, and predict pivotal feedback responses that might impact future climate states. This work focuses on developing a mechanistic understanding of how marine microbes respond to environmental fluctuations, and exploring how these individual-scale responses can result in large-scale ecosystem shifts and ecosystem-climate feedback loops. Untangling the complex interactions between climate and biology requires pioneering interdisciplinary approaches. The research will integrate ecological and evolutionary theory, and biological, chemical, and physical observations with innovative numerical ecosystem models, to gain new insight into the relationship between plasticity and evolution in marine microbial ecosystems.

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Andrew Alverson, Ph.D.

University of Arkansas

Andrew Alverson is an evolutionary biologist whose research combines phylogenetic, experimental, and evolutionary genomic approaches to identify the ecological and genomic factors driving the diversification of diatoms. He received his B.S. in Biology from Grand Valley State University in 1997, an M.S. from Iowa State University in 2000, and a Ph.D. from The University of Texas at Austin in 2006. For his Ph.D. research, Andrew studied the patterns and consequences of marine–freshwater transitions by diatoms, a diverse lineage of microalgae that produce some 20% of the earth's oxygen. From there he went on to Indiana University where he worked on the evolution of mitochondrial genome size in flowering plants with funding from a NIH NRSA Postdoctoral Fellowship. Andrew became an Assistant Professor in the Department of Biological Sciences at the University of Arkansas in 2011.
Project: The Genomic Basis of Microbial Adaptation to New and Changing Environments
Although evolutionary biology is a historical science, it provides a powerful means of looking forward as well—offering predictions on issues ranging from the spread of human disease to adaptation of species to global climate change. Increased atmospheric carbon and global warming are having profound impacts on the world's oceans. Changing precipitation patterns and melting polar ice caps are freshening large regions of the ocean, resulting in changes in water stratification, convection, and nutrient availability. Although these changes are predicted to have important impacts on the phytoplankton communities in these areas, relatively few data are available to predict how phytoplankton—which produce 40% of the earth's oxygen and form the base of marine food webs—will respond to a rapidly changing ocean. Laboratory experiments have shown that microbial eukaryotes can adapt quickly to environmental change in vitro, but it's not always clear how these results extrapolate to natural systems. This project leverages a natural evolutionary experiment, the colonization of low-salinity habitats in the Baltic Sea by an ancestrally marine diatom, Skeletonema marinoi, to determine the mechanisms and rate of adaptation to environmental stress across ecological and evolutionary timescales. Comparative and population genomic data, together with experimental transcriptomic data, will be combined to determine the tempo and mode of environmental adaptation of S. marinoi populations spanning the North–Baltic Sea salinity cline. Data from a related species, Skeletonema potamos, which has independently adapted to freshwaters, will show whether there is more than one adaptive solution to managing salinity stress, providing general insights into the adaptive potential of phytoplankton to a rapidly changing ocean.

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Otto X. Cordero, Ph.D.

University of Arkansas

Otto X. Cordero received a B.S. in Computer and Electrical Engineering from the Polytechnic University of Ecuador, an MSc in Artificial Intelligence from Utrecht University, and a PhD in Theoretical Biology also from Utrecht University. His main research focus is the ecology and evolution of natural microbial collectives. The Cordero lab is interested in understanding how social and ecological interactions at micro-scales impact the global productivity, stability and evolutionary dynamics of microbial ecosystems.
Project: Systems Ecology of Particle-Attached Microbial Communities in the Ocean
Bacteria play an essential role in the oceans by digesting particles of organic matter that would otherwise sink to the ocean floor and remove essential nutrients from the marine food web. At the micro-scale, particle degradation is carried out, not by a single species, but by a multi-species collective (i.e. a community) that grows attached to particle surfaces. Within these particle-attached communities there is a multitude of bacteria-bacteria interactions that can control the function and dynamics of the community, ultimately affecting the global ecosystem process. By and large, the nature of these interactions and their impact on community dynamics and ecosystem function remain unknown. This gap in our understanding of microbial ecology ultimately hampers the development of mechanistic models that explain how ecological function emerges from interactions within hyper-diverse microbial collectives.
This Simons Early Career Investigator Award will support the development of a systems ecology approach to the study of particle-attached communities in the ocean. Within this research program we will learn the general structure of ecological interaction networks on particles, and the classes of interactions that dominate the particle-attached community. We will learn for instance whether interactions are primarily exploitative, competitive or mutualistic, and how these different types of interactions impact the degradation dynamics. Overall, through this project we will establish the link between micro-scale community ecology to macro-scale ecosystem function in the ocean.

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Karen Lloyd, Ph.D.

University of Tennessee

Karen Lloyd is from Beaufort, North Carolina, and graduated from Swarthmore College with a degree in Biochemistry. She completed an MS and PhD in Marine Sciences at the University of North Carolina, and a postdoc at the Center for Geomicrobiology at Aarhus University, Denmark. She is currently an Assistant Professor at the University of Tennessee, where her research group studies the vast majority of marine subseafloor microorganisms that have never been grown in a laboratory, and are therefore mostly uncharacterized. Lloyd was awarded the Holger Hannasch Award from the Woods Hole Oceanographic Institution (2012), and the Alfred P. Sloan Fellowship (2015), and is an editor at mSystems.
Project: The role of uncultured microbes in the Arctic marine sediment carbon cycle
The Arctic is experiencing disproportionately large effects of global climate change and melting glaciers will likely deposit large amounts of organic carbon into Arctic coastal marine zones. Once this organic carbon is deposited on the seafloor, microbes quickly use up all the available oxygen, leaving the rest of the carbon cycle to anaerobic microbes. Little is known about the responses of the sedimentary microbial populations to this increasing organic carbon deposition. If anaerobic microorganisms living in the upper meter of Arctic marine sediments adapt quickly to the increase in organic matter, much of this organic matter will be remineralized back to CO2, driving a positive feedback on warming. On the other hand, if these populations cannot keep up with the influx of organic matter, organic matter burial rates will increase, driving a negative feedback on warming. Much of the microbial communities in Arctic sediments are unrelated to cultured microbes, so their potential role in organic matter remineralization is unknown. These types of organisms have been termed Microbial Dark Matter (MDM) since they are ubiquitous, enigmatic, and comprise some of the deepest evolutionary branches of life. I propose to use novel genetic, metabolic, and quantitative techniques to incorporate these MDM communities into models of carbon degradation in Arctic marine sediments in Svalbard, Norway.

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Jacob Waldbauer, Ph.D.

University of Chicago

Jacob Waldbauer is a Neubauer Family assistant professor in the Department of the Geophysical Sciences at the University of Chicago. His research combines field observations and laboratory experiments to explore the metabolic basis of biogeochemical fluxes, how microbial community response to environmental perturbations shapes biogeochemical feedbacks, and the molecular fossil record of past life and environments. His laboratory develops novel molecular analytical techniques, particularly using high-resolution mass spectrometry, to address outstanding questions in biogeoscience. He received a B.A. in Physics and Astronomy from Dartmouth College and a Ph.D. in Chemical Oceanography from the MIT/WHOI Joint Program, and was a Stanback/Beckman Postdoctoral Fellow at Caltech. He is the recipient of an Alfred P. Sloan Foundation Research Fellowship in Ocean Sciences and of the Cozzarelli Prize from the National Academy of Sciences.
Project: Forging the Missing Link: A Protein-Level View of Marine Microbial Ecology
Proteomic analysis — the identification of proteins in complex biological samples, and the quantification of protein-level gene expression — can enable quantitative, mechanistic connections between large-scale measurements of the chemical state of the oceans and of the genomic diversity in marine microbial ecosystems. In this project, we will use proteomics to gain new insights into two key aspects of marine microbial biogeochemistry: nitrogen limitation and anoxygenic phototrophy. Nitrogen availability is one of the most globally significant ecological pressures shaping the physiology and evolution of marine microbes, limiting primary production throughout much of the tropical and subtropical surface ocean. Since typically more than 80% of a cell’s nitrogen is in protein, N limitation is fundamentally a constraint on protein production, yet many questions remain about the molecular basis of this phenomenon in protein-level gene expression. Proteomic analysis can lend new insight into marine N limitation by quantification of community proteome abundance scales across spatial and temporal biogeochemical gradients. And while significant contributions of anoxygenic phototrophy to the metabolic energy budget of marine microbial communities (e.g., ATP production by proteorhodopsin-based phototrophy) have been hypothesized based on the abundance and diversity of sequences for these genes in marine metagenomic and metatranscriptomic datasets, testing this hypothesis has proven challenging. Measurement of the protein machinery that enables these metabolisms is a direct means to quantify their role in energy transduction. High-resolution proteomic measurements can also identify the primary organisms responsible for different modes of anoxygenic phototrophy in a range of oceanic habitats.

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Jake Bailey, Ph.D.

University of Minnesota – Twin Cities

Bailey is an interdisciplinary scientist who combines approaches from microbiology and the earth sciences to investigate interactions between the biosphere and geosphere, as well as to study the ecologies and physiologies of microorganisms that are involved in geobiological processes. Bailey is an assistant professor in the Department of Earth Sciences at the University of Minnesota, Twin Cities. He received his Ph.D. at the University of Southern California prior to receiving an Agouron Institute Geobiology Fellowship to support his postdoctoral research at Caltech. Bailey is an Alfred P. Sloan Foundation Research Fellow, University of Minnesota McKnight Land Grant Professor, and recipient of a National Science Foundation CAREER grant.
Project: Investigating the Microbiome of the Largest Known Bacteria
“Microbiome” is a term often given to the microbes associated with multicellular organisms, such as bacteria living in the human gut. While bacteria and archaea are known to live in association with other microbes, individual bacterial cells are not generally thought of as hosting a characteristic microbiome. My lab studies the largest known bacteria, Thiomargarita spp. These giant bacteria are involved in the biogeochemical cycling of carbon, sulfur, nitrogen, and phosphorus. They are also known for their involvement in the precipitation of calcium phosphate mineral deposits on the seafloor that are an important source of phosphorus for modern agriculture. Individual Thiomargarita cells can approach a millimeter in diameter, making them large enough to host extensive populations of other bacterial cells. New observations and molecular analyses suggest that smaller cells living in close association with Thiomargarita are important for the ecologies, physiologies, and biogeochemical influences of these giant bacteria. Interactions between Thiomargarita and other bacteria, as well as the biogeochemical influences they catalyze, will be investigated using a variety of interdisciplinary approaches ranging from genomics to geochemistry.

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Tanja Bosak, Ph.D.

Massachusetts Institute of Technology

Tanja Bosak was born in Croatia and graduated from the Zagreb University with a degree in Geophysics. After a summer of research at JPL and a short stint as a meteorologist at the Zagreb Airport, she moved to the California Institute of Technology in Pasadena, where she studied signatures of microbial processes in ancient sedimentary rocks and earned a Ph.D. in Geobiology. She spent two years at Harvard as a Microbial Initiative Postdoctoral Fellow, joined the Department of Earth, Atmospheric and Planetary Sciences at MIT in 2007 and is now an associate professor of Geobiology. Tanja's work integrates microbiology, sedimentology and stable isotope geochemistry into experimental geobiology to ask how microbes shape sedimentary rocks, how organisms fossilize and how microbial metabolisms leave biogeochemical patterns in sediments. Her lab uses this approach to explore modern biogeochemical and sedimentological processes and interpret the record of life on the Early Earth. For this work, and her work with graduate students and undergraduates, Bosak received the Subaru Outstanding Woman in Science award by the Geological Society of America (2007), the Macelwane Medal from the American Geophysical Union (2011), the Edgerton Award for young faculty at MIT (2012) and the Undergraduate Research Opportunities for Undergraduates Mentor of the Year award by MIT (2012). Bosak is a fellow of the American Geophysical Union (2011) and one of the subject editors of Geobiology.
Project: Record of Microbial and Geochemical Co-evolution in Cyanobacterial Genomes
Cyanobacteria have the longest and most continuous fossil record of all organisms. This fossil record is used to time events in the evolution of different cyanobacterial groups, as encoded by the genomes of modern cyanobacteria, and reveal links between ecological, evolutionary and geochemical changes on Earth’s surface. However, current time-calibrated models of cyanobacterial evolution (molecular clocks) rely on a simple fossil morphology whose cyanobacterial origin and taxonomic associations have been questioned. Furthermore, most taxonomically diagnostic cyanobacterial fossils represent benthic organisms, but the sampling of modern cyanobacterial genomes is biased toward unicellular planktonic taxa.
The work proposed here will improve the sampling of the cyanobacterial phylum and the understanding of its evolution through three major aims:

  1. To sequence and annotate the genomes of 40-60 undersampled, but geologically and environmentally relevant cyanobacterial taxa;
  2. To reconstruct major genomic events (gene additions, duplications and losses) in cyanobacterial history;
  3. To correlate these data with major events in Earth history and correlate events in cyanobacterial evolution with the evolution of other organismal groups which may lack a fossil record.

Sequencing efforts will use pure cultures from existing collections, or sorted cells/filaments from enrichment cultures and field samples. Modern homologs of the most taxonomically diagnostic and oldest unambiguous cyanobacterial fossils are not well represented in culture collections, so these samples will be obtained in the field. The newly sequenced genomes will be used to re-estimate divergence times using a relaxed molecular clock and new calibration points will be provided. Based on this analysis, genome reconciliation will be performed. The new cyanobacterial molecular clock will be used to correlate major gene acquisitions, losses and duplications with known events in Earth history or to hypothesize currently unknown events based on genomic data.

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Alyson Santoro, Ph.D.

University of California, Santa Barbara

Alyson Santoro is an assistant professor in the Department of Ecology, Evolution, and Marine Biology at the University of California, Santa Barbara. She received a B.A. from Dartmouth College in Ecology and Evolutionary Biology and an M.S. and Ph.D. from Stanford University in Environmental Engineering and Science. She was the recipient of the Woods Hole Oceanographic Institution Postdoctoral Scholar Fellowship for her research in nitrogen isotope geochemistry. Her research combines sea-going and laboratory investigations of marine microbes, with an emphasis on marine archaea and their role in the nitrogen cycle. She is the recipient of a Sloan Foundation Early Career Fellowship in Ocean Sciences.
Project: Growth Efficiency in the Mesopelagic at Station ALOHA
Organic carbon sinking from the ocean’s surface can meet three fates in the dark waters below: it can be assimilated into biomass, respired back to carbon dioxide, or continue sinking to the seafloor. Quantifying these fates—the ocean’s biological pump—is essential to constructing a carbon and energy budget for the ocean’s interior, and predicting changes in this budget into the future. The growth efficiency of microorganisms, that is, what fraction of the carbon they consume becomes cellular biomass, is an essential parameter to developing balanced budgets of carbon storage in the ocean’s interior. I will use novel cultivation techniques to establish bacterial and archaeal culture systems for understanding carbon, nitrogen, and energy flow in the mesopelagic at Station ALOHA. Efforts will be directed at determining quantitative physiological parameters such as growth efficiencies, substrate affinities, and temperature optima that can feed directly into predictive models of microbial ecosystem structure and function. By combining laboratory experiments, in situ experimentation, and time-series measurements of material export and microbial standing stocks, the SCOPE initiative provides a unique opportunity to undertake a systematic and integrated study of microbial growth efficiency in the mesopelagic at unprecedented resolution. The ultimate goal of this work is to construct an energy budget for the mesopelagic to understand and predict the efficiency of the biological pump.

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Frank Stewart, Ph.D.

Georgia Institute of Technology

Frank Stewart is a marine microbiologist with broad interests in the genetic and metabolic diversity of ocean bacteria. His lab uses the tools of genomics and molecular biology to understand how marine microbes respond to environmental change and to symbiotic interactions with other organisms. In particular, research in the lab explores the diversity, evolution, and function of symbioses between bacteria and marine animals. This work targets diverse interactions, including those between deep-sea invertebrates and intracellular bacteria, as well as those within multi-species microbiomes on the surfaces and in the guts of reef corals and fish. The lab employs genomic and meta-omic methods to study these associations, often in collaboration with biogeochemists and ecologists. A second major research theme in the lab seeks to understand how declines in ocean oxygen content, due in part to climate change, affect microbial diversity and elemental cycling. This work focuses on major low-oxygen water masses in the Gulf of Mexico and the eastern Pacific Ocean, and involves a combination of oceanographic sampling, community genomics, biogeochemistry, and bioinformatics.
Dr. Stewart is an assistant professor in the School of Biology at Georgia Tech. He received a B.A. in Biology from Middlebury College and a Ph.D. in Organismic and Evolutionary Biology from Harvard University. He worked as a Postdoctoral Fellow at MIT before moving to Georgia Tech in 2011. He is a recipient of a Sloan Research Fellowship in Ocean Sciences and a Faculty Early Career Development Award from NSF.
Project: Reef Fish Microbiomes: Models for Bacteria-Host Interaction in the Ocean
Animals harbor diverse and abundant microbial communities (microbiomes) that influence key aspects of host health, development, and behavior. The ecology and evolution of microbiomes remain almost completely unexplored for the largest and most diverse of the vertebrate groups, the teleost fishes. Coral reefs in particular support one of the richest assortments of fish among the major ocean ecosystems, with over 2500 species spanning a striking diversity of niches, reproductive and parental care strategies, and diet types. Reef fish microbiomes are hypothesized to harbor a wide diversity of uncharacterized bacterial lineages with potentially important roles as mediators of fish nutrition and disease prevention and as reservoirs for free-living or coral microbiome populations. The overarching goal of this project is to characterize the reef fish microbiome as a model for understanding microbe-animal interactions in the ocean. The research involves a combination of field sampling and laboratory experiments to understand the diversity of the reef fish microbiome and its relationship to host ecology and development, genomic analyses to identify key physiological properties and novel members of the microbiome, and experiments to quantify transmission routes of fish microbiomes and potential microbiome effects on fish behavior. This integrated approach will help identify connections between fish-associated and other microbial niches on reefs, as well as benefits of microbial-association, potentially including unrecognized contributions to fish immunity, digestion, and chemical signaling between individuals.

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