Message from the Managing Director:

Being a part of C-DEBI has been a huge part of my life. I truly enjoyed getting to know so many of you and supporting the framework for moving deep biosphere research and education programs forward in our Center’s 12 years. As C-DEBI comes to an end officially at the end of September, there are various transitions happening at the same time. As many of you know, I have joined the COBRA-AccelNet team (with overlapping C-DEBI Leadership by Beth Orcutt, Julie Huber, Andy Fisher and Geoff Wheat), so after C-DEBI ends, you can find me on the Bigelow Laboratory staff. In the meantime, I’ll be wrapping up C-DEBI after my upcoming maternity leave starting in mid-August. This won’t be our last communication, but with all these moving parts, there will be a few newsletters on hiatus.

To keep those of you interested in the deep biosphere engaged in the future, we will be migrating all on the C-DEBI newsletter to the COBRA newsletter where we will share similar content related to the crustal biosphere monthly. If you aren’t interested, unsubscribe when you receive the first newsletter in the next month.

Hope to cross paths with you again someday, somewhere!
Rosalynn Sylvan
C-DEBI Managing Director

Thank you to all for being a part of C-DEBI through the Virtual Meeting Series. C-DEBI nurtured a community of deep biosphere experts, and that expertise is urgently needed to inform new emerging uses of the deep sea, especially in the rocky parts of the deep sea, such as potential removal of rocks for industrial mineral interests or using the deep sea as a repository for carbon dioxide to address global warming. This has led to the initiation of the COBRA program, a new research coordination network with the mission to accelerate the research on these types of topics, so that scientists can inform decision making. Sign up for the COBRA newsletter to stay connected to the webinar series launching soon as part of the COBRA mission to help with coordination, knowledge sharing and training of all of us who care about microbes in the deep sea with policymakers.

Did you miss the last VMS on The Many Ways to Use Anvi’o, a Platform for Microbial ‘Omics? Check out the recording with invited speaker Iva Veseli (University of Chicago) as she introduces Anvi’o, a community-driven software platform enabling integrated analyses and interactive visualization of multi-’omic data, and discusses the various ways to learn and use anvi’o, and how these strategies fit different research needs and users with different levels of computational experience.

Friday June 3, 2022 (9:30 – 11:00AM Pacific Time)

The Many Ways to Use Anvi’o, a Platform for Microbial ‘Omics
Iva Veseli (University of Chicago)

Cheaper, higher-quality sequencing technologies have made ‘omics analyses – metagenomics, pangenomics, phylogenomics, and more – central to investigations of microbial ecology and evolution. Anvi’o is a community-driven software platform enabling integrated analyses and interactive visualization of these multi-’omic data. It offers a versatile set of programs for working with sequence data that researchers can mix and match according to their research questions. While this can present a steeper learning curve than a simple data-in-results-out pipeline, it is not as difficult as you might think. We will discuss the various ways to learn and use anvi’o, and how these strategies fit different research needs and users with different levels of computational experience.

Register in advance of the meeting for connection information.

Friday May 6, 2022 (9:30 – 11:00AM Pacific Time)

Living at the Extremes: Extremophiles and the Limits of Life in a Planetary Context
Nancy Merino (Lawrence Livermore National Laboratory)
Diana Bojanova (University of Southern California)
Michael Wong (Carnegie Institution for Science)

In the context of prokaryotic life, extremophiles are microorganisms that thrive under harsh conditions, including pH, temperature, salinity, and pressure. In fact, many extremophiles persist under multiple extremes and are known as polyextremophiles. Research on extremophiles has revealed key microbial adaptations to extreme environments and enabled us to hypothesize about the origins and evolution of life on Earth. This research also has implications for assessing the feasibility and the search for life on other planetary and celestial bodies. In this virtual meeting, Nancy Merino (Lawrence Livermore National Laboratory), Diana Bojanova (University of Southern California), and Michael Wong (Carnegie Institution for Science) will discuss their paper titled “Living at the Extremes: Extremophiles and the Limits of Life in a Planetary Context” (written with co-authors Heidi Aronson, Jayme Feyhl-Buska, Shu Zhang and Donato Giovannelli) in which they review the biospace that life operates on Earth and the potential for life elsewhere.

Register in advance of the meeting for connection information.

Did you miss the last VMS on Sampling Oceanic Crustal Fluids: Some Options? Check out the recording with invited speakers Rika Anderson (Carleton College), Julie Huber (Woods Hole Oceanographic Institution), Susan Lang (University of South Carolina), and Michael Rappé (University of Hawaii) as they discuss the many different types of samplers including those available for sampling hydrothermal fluids with submersibles, and the costs and benefits of the different approaches.

Friday March 4, 2022 (9:30 – 11:00AM Pacific Time)

Sampling Oceanic Crustal Fluids: Some Options
Rika Anderson (Carleton College)
Julie Huber (Woods Hole Oceanographic Institution)
Susan Lang (University of South Carolina)
Michael Rappé (University of Hawaii)

The fluids that circulate through the oceanic crust can provide valuable windows to the microbiology and geochemistry of the subseafloor, but can be challenging to collect in sufficient volume and without contamination. We will discuss the many different types of samplers including those available for sampling hydrothermal fluids with submersibles, and the costs and benefits of the different approaches.

Register in advance of the meeting for connection information.

Friday February 4, 2022 (9:30 – 11:00AM Pacific Time)
METABOLIC Bioinformatics Tool
Karthik Anantharaman, Zhichao Zhou, and Patricia Tran (University of Wisconsin)

In the recent decade, metagenomics and single-cell genomics have significantly changed our understanding of the microbial world, especially uncultured microbial taxa. While advanced genomic approaches have allowed scientists to discover a rich diversity of microorganisms from diverse settings, bioinformatic tools which could help us to interpret and organize genomic blueprints into metabolism and biogeochemistry at the individual and community scales are necessary to facilitate research in diverse fields. METABOLIC is a newly developed scalable metabolic and biogeochemical functional trait profiler to comprehensively study microbial metabolism and interactions using genome data.

In this talk, we will present the capabilities of METABOLIC that can enable (1) Metabolic and biogeochemical analyses for genomes and microbial communities, and (2) Visualization of biogeochemical cycling potential and community-scale functional networks.

Register in advance of the meeting for connection information.

Building from the foundation of C-DEBI, a new NSF-funded network-of-networks started this fall called COBRA – the Crustal Ocean Biosphere Research Accelerator. The goal of COBRA is to generate new knowledge on the structure, function, resilience, and ecosystem services of the crustal ocean biosphere – life attached to the rocks at the bottom of the ocean – to inform decision-making relating to emergent industrial uses of the deep ocean, such as deep-sea mining and subseafloor carbon sequestration, and decrease the likelihood of serious harm to the environment while maintaining the broad benefits that society currently enjoys. COBRA will help to close knowledge gaps by bringing together stakeholders through virtual workshops and supporting cross-coordination and collaboration. As a global community of experts in deep sea and subseafloor deep biosphere science, the C-DEBI community is uniquely poised to make great contributions to COBRA efforts. Join this virtual meeting series to hear from COBRA Director Dr. Beth Orcutt and COBRA Associate Director Dr. Julie Huber (also both C-DEBI scientists) to learn more about how you can get involved and take advantage of opportunities. Register in advance of this meeting on January 7, 2022 (9:30 – 11:00AM Pacific Time).

Field work is often viewed as a career highlight, shaping the trajectories of graduate students and early career researchers. Negative experiences in the field, intimidating behaviors (including hazing, bullying), harassment, discriminatory behaviors, gendered division of labor, and assault, can have severe consequences for victims and their careers. In this event, Dr. Ivona Cetinić (NASA Goddard) will discuss ways to create a safe and productive field climate, focusing on the role that PIs play in setting expectations for (and rules of) behavior, and the accountability for violations. Register in advance of this meeting on December 3, 2021 (9:30 – 11:00AM Pacific Time).

Message from the Director:

We enjoyed a final, final Annual Meeting in person last month in Marina, CA with great talks and discussions amongst the company of friends and colleagues we’ve interacted with over a decade of C-DEBI.  Thank you to each and every one of the nearly 1000 participants who has contributed to the success of the Center’s research, education, outreach, diversity, and knowledge transfer!

Coming up Friday at 9:30-11AM Pacific is our last Virtual Meeting Series event of the year with Ivona Cetinič (NASA Goddard): How to Better Prepare Participants and Mentors for Preventing/Addressing Sexual Harassment in the Field.

Happy holidays and best wishes for the new year!

Cheers,

Jan Amend
C-DEBI Director

Message from the Director:

A sincere congratulations to C-DEBIer Jen Biddle (University of Delaware) who will receive the Joanne Simpson Medal for Mid-Career Scientists from the American Geophysical Union in recognition of her transformative scientific advances in the Earth sciences, demonstrated strong leadership, and outstanding service to science and society. Please share your personal kudos if you will also be attending the AGU Fall Meeting in New Orleans or online in December.

Cheers,

Jan Amend
C-DEBI Director

Our next virtual meeting features  Marisela Martinez-Cola (Morehouse College) who will present “Collectors, Nightlights, & Allies, Oh My! : Advice for Strengthening Cross-racial Mentoring Relationships” on Friday, October 1, 2021 (10:30AM – 12:00PM Pacific Time). The virtual meeting series is held monthly during the first week of each month, with a regular rotation of science workshops and professional development workshops. Each workshop will contain about 90 minutes of programming, including invited speakers to give plenary tutorials and presentations, breakout icebreaker and discussion sessions, and plenary Q&A sessions. Register in advance for the meeting on October 1, 2021.

Mark your calendars for the next virtual meeting “The Future of MBIO in IODP” on September 3, 2021 (10:30AM – 12:00PM Pacific). Do you have questions about how deep biosphere/microbiology sampling is part of the international scientific ocean drilling program (the International Ocean Discovery Program, IODP), and how subseafloor samples are collected? Have you wondered how you can get more involved with IODP, or how proposals for drilling are handled? Are you curious about the future of IODP beyond the current program, and how deep biosphere/microbiology science can be part of that future?

This C-DEBI Virtual Meeting Series event will feature a panel of deep biosphere scientists highlighting these topics and answering your questions. Everyone is welcome to join – from experienced IODP users to those who have never been involved with IODP. Panelists will include Jennifer Biddle (University of Delaware), Stephanie Carr (Hartwick College), Steven D’Hondt (University of Rhode Island Graduate School of Oceanography), Jessica Labonté (Texas A&M University Galveston), Beth Orcutt (Bigelow Laboratory for Ocean Sciences), and Jason Sylvan (Texas A&M University).

The virtual meeting series is held monthly during the first week of each month, with a regular rotation of science workshops and professional development workshops. Each workshop contains about 90 minutes of programming, including plenary presentations by invited speakers, a community building breakout session, and a plenary Q&A session.

Cheers,

C-DEBI Virtual Series Meeting Organizers:
Joy Buongiorno, Maryville College
James Bradley, Queen Mary University of London
Beth Orcutt, C-DEBI Senior Scientist, Bigelow Laboratory for Ocean Sciences
Rosalynn Sylvan, C-DEBI Managing Director, University of Southern California

Do you have questions about how deep biosphere/microbiology sampling is part of the international scientific ocean drilling program (the International Ocean Discovery Program, IODP), and how subseafloor samples are collected? Have you wondered how you can get more involved with IODP, or how proposals for drilling are handled? Are you curious about the future of IODP beyond the current program, and how deep biosphere/microbiology science can be part of that future?

This Virtual Meeting Series event will feature a panel of deep biosphere scientists highlighting these topics and answering your questions. Everyone is welcome to join – from experienced IODP users to those who have never been involved with IODP. Panelists will include Jennifer Biddle (University of Delaware), Stephanie Carr (Hartwick College), Steven D’Hondt (University of Rhode Island Graduate School of Oceanography), Jessica Labonté (Texas A&M University Galveston), Beth Orcutt (Bigelow Laboratory for Ocean Sciences), and Jason Sylvan (Texas A&M University).

Register in advance for the meeting on September 3, 2021.

Building from the foundation of C-DEBI, a new NSF-funded network-of-networks called COBRA – the Crustal Ocean Biosphere Research Accelerator– is spinning up this fall to bring together diverse stakeholders to accelerate research on the structure, function, resilience, and ecosystem services of the crustal ocean biosphere to inform decision making. The goal is to generate new knowledge and inform decision-making relating to emergent industrial uses of the deep ocean, such as deep-sea mining and subseafloor carbon sequestration, and decrease the likelihood of serious harm to the environment while maintaining the broad benefits that society currently enjoys. COBRA will help to close knowledge gaps by facilitating coordination of expedition and observatory efforts and dissemination of white papers generated through virtual workshops. In collaboration with international partners and leveraged expeditions of COBRA participants, COBRA will support an international early career researcher virtual expedition leadership training program, helping to build the community of experts engaged in deep-sea exploration, science, and policy. COBRA will also support international research exchanges for early career researchers wanting to engage in crustal ocean biosphere research to inform policy. All training efforts will be designed to promote team science collaboration, diversity, equity, and inclusivity.

COBRA will be led by C-DEBI Senior Scientists Beth Orcutt, Julie Huber, Andy Fisher, and Geoff Wheat along with Jim McManus and Randi Rotjan and managed by C-DEBI Managing Director Rosalynn Sylvan. As a global community of experts in deep sea and subseafloor deep biosphere science, the C-DEBI community is uniquely poised to make great contributions to COBRA efforts. COBRA officially launches October 1. Stay tuned for more details about how to get involved and find out more here!

Techniques for Isolating Persnickety Microbes

Our next virtual series meeting features plenary speakers Roman Barco (University of Southern California) and Ileana Pérez-Rodríguez (University of Pennsylvania) who will present on Friday August 6 (10:30AM – 12:00PM Pacific). The virtual meeting series is held monthly during the first week of each month, with a regular rotation of science workshops and professional development workshops. Each workshop will contain about 90 minutes of programming, including invited speakers to give plenary tutorials and presentations, breakout icebreaker and discussion sessions, and plenary Q&A sessions. Register in advance for the meeting on August 6, 2021.

Our next virtual meeting features plenary speakers Roman Barco (University of Southern California) and Ileana Pérez-Rodríguez (University of Pennsylvania) who will present on Friday August 6 (10:30AM – 12:00PM Pacific). The virtual meeting series is held monthly during the first week of each month, with a regular rotation of science workshops and professional development workshops. Each workshop will contain about 90 minutes of programming, including invited speakers to give plenary tutorials and presentations, breakout icebreaker and discussion sessions, and plenary Q&A sessions. Register in advance for the meeting on August 6, 2021.

Our next virtual meeting features plenary speaker Jackie Goordial (University of Guelph) who will present “Squeezing DNA from a rock: DNA extractions from low biomass settings” on Friday July 9 (10:30AM – 12:00PM Pacific). The virtual meeting series is held monthly during the first week of each month, with a regular rotation of science workshops and professional development workshops. Each workshop will contain about 90 minutes of programming, including invited speakers to give plenary tutorials and presentations, breakout icebreaker and discussion sessions, and plenary Q&A sessions. Register in advance for the meeting on July 9, 2021.

Did you miss the last VMS “Building Capacity for a Thriving Research Lab at a PUI (Primarily Undergraduate Institution)“?  We’ve posted the presentations by plenary speakers Rika Anderson (Carleton College) and Terry McGlynn (California State University Dominguez Hills), as well as a variety of other resources identified by meeting participants including online communities with a focus on Science at PUIs.

Mark your calendars for the next virtual meeting “Techniques for Isolating DNA from Tough Samples” on July 9, 2021 (10:30AM – 12:00PM Pacific). This VMS features plenary speaker Jackie Goordial (University of Guelph) who will present “Squeezing DNA from a rock: DNA extractions from low biomass settings”.

The virtual meeting series is held monthly during the first week of each month, with a regular rotation of science workshops and professional development workshops. Each workshop contains about 90 minutes of programming, including plenary presentations by invited speakers, a community building breakout session, and a plenary Q&A session.

Cheers,

C-DEBI Virtual Series Meeting Organizers:
Joy Buongiorno, Maryville College
James Bradley, Queen Mary University of London
Beth Orcutt, C-DEBI Senior Scientist, Bigelow Laboratory for Ocean Sciences
Rosalynn Sylvan, C-DEBI Managing Director, University of Southern California

How to Build Capacity for a Thriving Research Lab at a PUI (Primarily Undergraduate Institution)

Our next virtual series meeting features plenary speakers Rika Anderson (Carleton College) who will present “Conducting research with undergraduates at a small liberal arts college” and Terry McGlynn (California State University Dominguez Hills) who will present “How to develop an undergraduate research lab with long-term sustainability”. Register in advance of the meeting on Friday June 4 (10:30AM – 12:00PM Pacific). The virtual meeting series is held monthly during the first week of each month, with a regular rotation of science workshops and professional development workshops. Each workshop contains about 90 minutes of programming, including plenary presentations by invited speakers, a community building breakout session, and a plenary Q&A session.

Our next virtual meeting features plenary speakers Rika Anderson (Carleton College) who will present “Conducting research with undergraduates at a small liberal arts college” and Terry McGlynn (California State University Dominguez Hills) who will present “How to develop an undergraduate research lab with long-term sustainability” on Friday June 4 (10:30AM – 12:00PM Pacific). The virtual meeting series is held monthly during the first week of each month, with a regular rotation of science workshops and professional development workshops. Each workshop will contain about 90 minutes of programming, including invited speakers to give plenary tutorials and presentations, breakout icebreaker and discussion sessions, and plenary Q&A sessions. Register in advance for the meeting on June 4, 2021.

Our next virtual meeting features plenary speaker Roland Hatzenpichler (Montana State University) who will present “Next-generation physiology: Why and how to measure microbial phenotypes under (close to) in situ conditions” on Friday May 7 (10:30AM – 12:00PM Pacific). The virtual meeting series is held monthly during the first week of each month, with a regular rotation of science workshops and professional development workshops. Each workshop will contain about 90 minutes of programming, including invited speakers to give plenary tutorials and presentations, breakout icebreaker and discussion sessions, and plenary Q&A sessions. Register in advance for the meeting on May 7, 2021 (10:30AM – 12:00PM Pacific).

Join us Monday, April 5, 2021 (10:30AM – 12:00PM Pacific Time) for the inaugural C-DEBI Virtual Meeting on New Tools in Bioinformatics. Building on the enthusiasm of our first virtual annual meeting in 2020, we continue to bring the C-DEBI community together through a virtual meeting series. These virtual events will be held monthly during the first week of each month, with a regular rotation of science workshops and professional development workshops. Each workshop will contain about 90 minutes of programming, including invited speakers to give plenary tutorials and presentations, breakout sessions, and plenary Q&A sessions.

This meeting on new tools in bioinformatics will include plenary speakers:

Dr. Ben Tully, University of Southern California
EukMetaSanity: A customizable workflow for the gene prediction and annotation of Eukaryotic genomes

Dr. Jake Weissman, University of Southern California
Estimating maximal microbial growth rates from cultures, metagenomes, and single cells via codon usage patterns

Message from the Director:

Congratulations to the Reach Out Science Communication Challenge semi-finalists from C-DEBI: Sabrina Elkassas (MIT-WHOI) and Rachel Weisend (Texas A&M Corpus Christi)! Cheer them on as they compete among 18 others in the Reach Out Semifinals live tentatively on April 13 (4PM Pacific) to the panel of expert science communicator judges: Raven Baxter, Emily Calendrelli, Jorge Cham, and Melissa Cristina Márquez. More details to come.

We are also pleased to announce the inaugural event for our C-DEBI Virtual Meeting Series based on your enthusiasm for C-DEBI community activities at our last annual meeting. Ben Tully (USC) and Jake Weissman (USC) will kick off the series on new tools in bioinformatics on Monday April 5 (10:30AM – 12:00PM Pacific). Save the date for this first of our virtual events to be held monthly during the first week of each month, with a regular rotation of science workshops and professional development workshops. Each workshop will contain about 90 minutes of programming, including invited speakers to give plenary tutorials and presentations, breakout sessions, and plenary Q&A sessions. Stay tuned for more information.

Don’t forget to also tune in to our final C-DEBI Networked Speaker Series talk “Outwit, Outplay, Outlast: A microbial tale of survival within the marine deep subsurface” presented by Megan Mullis (Texas A&M University at Corpus Christi) on March 18 at 12:30PM Pacific Time.

Cheers,

Jan Amend
C-DEBI Director

Megan Mullis, Texas A&M Corpus Christi, will present “Outwit, Outplay, Outlast: A microbial tale of survival within the marine deep subsurface” in the next Networked Speaker Series live on March 18, 2021, 9:30am HAST/ 12:30pm PST / 3:30pm EST.

Abstract: Microbes play fundamental roles in ecosystem function through mediating biogeochemical cycles, yet we know very little about how microbes interact and what drives community diversity. The marine deep subsurface hosts a massive reservoir of microbial biomass that can be actively surviving (or even thriving) harsh conditions, such as high pH, low nutrients, or extreme temperatures. There are various methods to analyze microbial community diversity and functionality within the marine subsurface including culture-independent and -dependent methods. The studies presented here utilize this two-pronged approach to investigate microbial diversity, functionality, and specific survival mechanisms within two marine subsurface environments. The Mariana Forearc sediments were sampled through use of the International Ocean Discover Program Expedition 366 from December 2016 – February 2017. Sediments were extracted for total RNA as a proxy for microbial activity and sequenced using Illumina NovaSeq. These metatranscriptomes were analyzed for microbial diversity and metabolic capabilities and indicates microbial life is persisting through partial denitrification (nirKS) and anaerobic methane oxidation (pmoABC). The western flank of the Mid-Atlantic Ridge (commonly referred to as North Pond) sediments were sampled via push cores aboard the R/V Atlantis in October 2017. We utilized a novel method of high-throughput single-cell sorting using Fluorescence Activated Cell Sorting (FACS) to cultivate individual cells from shallow North Pond sediments. Individual cells from sediment slurries were sorted into a modified artificial seawater medium and extracted for whole genome sequencing using Illumina MiSeq. I will present novel methodology and genome characterizations from Idiomarina abyssalis strain KJE, Marinobacter salarius strain NP2017, and Marinobacter salarius strain AT3901.

We are happy to be able to offer the Global Environmental Microbiology course in summer 2021. Our plan is to host this course in-person at the University of Southern California (University Park Campus) and on Santa Catalina Island from Sunday, June 13 through Friday, July 2. However, if we cannot host the course in-person, we will offer a highly modified version of the course online from Monday, June 14 through Friday, July 2. We hope to know in mid-spring 2021 if it will be possible to hold the program in-person. Applications are closed.

The Center for Dark Energy Biosphere Investigations (C-DEBI), headquartered at the University of Southern California (USC) and funded by the National Science Foundation (NSF), is offering an all-expense paid, three-week, intensive introductory aquatic microbiology course called Global Environmental Microbiology (GEM).

We are recruiting early career undergraduates interested in a STEM career from 2- and 4-year colleges:

• to join us at the University of Southern California and Santa Catalina Island
• from June 13 through July 2, 2021
• for lectures, discussions, labs, fieldwork, networking, career panels and more
• focusing on aquatic microbes and their ecology
• taught by Drs. John Heidelberg and Eric Webb
• paid for by C-DEBI, including travel, room, board, and course expenses

HOWEVER, if we cannot offer an in-person program in summer 2021, we will offer a highly modified online version of the course: Summer OnLine Interactive/Discussion-Global Environmental Microbiology (SOLID-GEM).

We strive to recruit participants that reflect the diversity of students at the community college and university level with varied science learning and life experiences. We encourage students from groups underrepresented in STEM fields and first-generation college students to apply.

Application Deadline: February 25, 2021 at 5:00pm PST

For questions and comments, contact Gwen Noda at gnoda@usc.edu.

Message from the Director:

C-DEBI 2020 Annual Meeting participants pose for a group screenshot

It’s been 10 amazing years as an NSF Science and Technology Center (STC), and we continue to phase down in the next 2 years under a no-cost extension. We now come to the time to say thank you and goodbye to members of our staff who have supported the C-DEBI community, programs and activities that have been integral to our success: Matt Janicak (Data Manager and Webmaster); Nerissa Rivera-Laux (Administrative Assistant); and Gwen Noda (Education and Diversity Director) who is transitioning into the Wrigley Institute at USC while the undergraduate GGURE and GEM programs finish this coming spring/summer. Rosalynn Sylvan (Managing Director) will continue to manage the administration of C-DEBI, so please keep her listed as your primary contact.

We also share here an STC-only student and postdoc opportunity “Reach Out Science Communication Challenge” hosted by the NSF and the Boston Museum of Science. Current C-DEBI-affiliated undergraduate, graduate student, and postdoctoral researchers are invited to participate in 2 free virtual science communication workshops in January to sharpen their public communication skills with students and postdocs from all 12 STCs ($50 stipends are earned by attending both workshops and responding to follow-up surveys). Competitive “Reach Out Science Slams” in the spring will be nationally live-streamed with additional prizes. More information including eligibility, rules, and guidance at https://www.mos.org/reach-out-challenge.

Cheers,

Jan Amend
C-DEBI Director

With Dr. Julia McGonigle, Bigelow Laboratory for Ocean Sciences on “Formate metabolism by Chloroflexi is key in unlocking deep carbon for the Lost City chimney ecosystem.” Abstract: The Lost City hydrothermal field on the Mid-Atlantic Ridge supports dense microbial life on towering calcium carbonate chimney structures. This microbial life is fueled by chemical reactions between the ultramafic rock under the chimneys and ambient seawater. These serpentinization reactions provide reducing power (as hydrogen gas) and organic compounds that can serve as microbial food. Previous studies have characterized the interior of the chimneys as a single-species biofilm inhabited by the Lost City Methanosarcinales, but genomic evidence indicating this methanogen is able to metabolize the most abundant carbon source (formate) is lacking. I will present recent metagenomic results that suggest the non-formate utilizing species inhabiting Lost City chimney biofilms might rely on carbon-cycling activity of a Chloroflexi population. I will also present current comparative genomic work on a distantly-related Chloroflexi population, obtained through hydrothermal fluid sampling, suspected to reside in the subsurface habitat under the Lost City chimneys.

Message from the Director:

We hope this fall semester treats you safe and well. We also congratulate these C-DEBIers who have recently been promoted or are starting new positions: Brandon Briggs (Associate Professor at University of Alaska Anchorage); Joy Buongiorno (Assistant Professor at Maryville College); Jackie Goordial (Assistant Professor at the University of Guelph); Jeff Marlow (Assistant Professor at Boston University); Bill Orsi (Associate Professor at LMU Munich); Brandi Reese (Associate Professor at Dauphin Island Sea Lab); Haley Sapers (Assistant Professor at York University); Lauren Seyler (Assistant Professor at Stockton University); Jason Sylvan (Associate Professor at Texas A&M University); and Katrina Twing (Assistant Professor at Weber State University).

And stay tuned for our next season of Networked Speaker Series talks! Dr. Rose Jones (University of Minnesota) kicks it off with “Menu for a deep microbe: Attempts in understanding microbe-mineral interactions in the deep marine seafloor” on September 10 at 12:30PM Pacific Time. Our other distinguished speakers include Dr. Julia McGonigle (Bigelow), Dr. Jesse Colangelo-Lillis (CU Boulder), and Megan Mullis (Texas A&M Corpus Christi).

Cheers,

Jan Amend
C-DEBI Director

With Dr. Rose Jones, University of Minnesota on “Menu for a deep microbe; attempts in understanding microbe-mineral interactions in the deep marine seafloor.” Abstract: For microbes in the deep marine subsurface, inorganic chemical energy often is the sole energy source, catalyzing redox reactions of chemical species dissolved in fluid or from solid substrate. This influences the environment by altering subsurface minerals and geochemistry. I’m currently looking for evidence of how microbes influence mineralogy at East Pacific Rise 9.5°N, using Synchrotron microprobe X-ray fluorescence mapping (XRF), X-ray diffraction (XRD), and X-ray absorption spectroscopies (XAS) to map element distributions and phase identification for crystalline and poorly-crystalline minerals. With this information we can describe how minerals change in space and time during the transition from active to inactive venting, providing context for understanding microbial community patterns. Using bioelectrochemistry, I also found evidence of microbes capable of influencing cool, oxic basalt at North Pond, Mid-Atlantic ridge through directly transferring electrons from the minerals. Overall, our results are attempting to understand how microbes and minerals influence each other and local geochemistry in the deep marine seafloor.

Message from the Director:

Due to the lingering challenges surrounding the COVID-19 pandemic, we have decided to postpone this fall’s C-DEBI annual meeting to 2021. However, to maintain a connection with members of the C-DEBI community to present active research projects and support integrated discussions, we are considering a virtual meeting in November and will invite your ideas / suggestions / interest in the coming weeks.

Cheers and be safe,

Jan Amend
C-DEBI Director

Message from the Associate Director:

I recently read an article in The New Yorker about deep-sea exploration that made my blood boil and my heart sink. In response, I wrote a letter to the editor, copied below and posted to Twitter. We can do better.

Julie Huber
C-DEBI Associate Director

20 May 2020

Dear Editor,

As I was reading Ben Taub’s piece about a millionaire’s deep-sea journey, I felt a familiar swell of rage building as paragraph-after-paragraph, another man’s backstory was told, shrouded in white privilege and machismo (A Reporter At Large, May 18th). By the end, I realized that I felt as I sometimes do as the only female scientist in the room: left out and turned off.

Ocean science and engineering, like most STEM fields, suffers from a lack of diversity, and many of us are working hard to bring underrepresented voices to our labs, research cruises, and outreach efforts. This story sets us back. While some of the accomplishments of the Five Deeps team are certainly worth highlighting, we must find ways to tell such stories without celebrating the millionaire maverick explorer of European descent striving for records with little technical expertise and a general disregard for safety.

Many barriers exist to creating a culture of inclusion and equity in oceanography, but the portrayal of deep-sea exploration in this story reflect the fields’ origins, and it is no longer the reality of modern oceanographic research nor the future we strive for. Given the state of our world and the importance of science and engineering to our society, we must recruit, retain and mentor a diverse and talented community of future STEM participants that can work in our highly collaborative and team-oriented field. The ocean (our planet, our society) deserve better.

Julie Huber, PhD
Falmouth, MA

Message from the Associate Director:

This past week, I participated in a national #Strike4BlackLives to support the Black Lives Matter movement and condemn institutional racism in academia and science. Based on my twitter feed, it looks like many of our C-DEBI community members did as well. In Woods Hole, a small town with a big scientific impact, we organized a protest march and asked community members to stop business as usual to reflect on anti-black racism in America, recognize ways academia perpetuates harmful narratives, and plan ways to stop injustice. Beyond the march, I also spent time reading about hiring bias in academia, looking at statistics for our academic programs at WHOI, and listening to stories from local Black community members on their experiences here. On Twitter, I saw C-DEBI community members making donations, writing Wikipedia pages for Black scientists and “lab values” statements for their groups, reaching out to their local societies for support and resources, and developing many other future plans for confronting racism in STEM.

I encourage all of the C-DEBI community to support efforts against racism in the scientific community and society at large. While there are many resources and potential actions, this one day movement provided an excellent start for those eager to participate and educate themselves.

Learn more about #Strike4BlackLives / #ShutDownSTEM:

• #ShutDownSTEM: Resources
• Particles For Justice

National coverage of the events:

• Science: Researchers around the world prepare to #ShutDownSTEM and ‘Strike For Black Lives’
• Nature: Thousands of scientists worldwide to go on strike for Black lives
• Wired: Across the Globe, Scientists Are Striking for Black Lives

And from my neck of the woods:

• WCAI/NPR: Local Scientists Confront Racism in Their Ranks

Julie Huber,
C-DEBI Associate Director

The GEM Course is an all-expenses paid, three-week intensive introductory course in Global Environmental Microbiology (GEM) geared toward early-career undergraduates from 2- and 4-year institutions. The course focuses on microbes found in aquatic environments investigated through authentic research experiences (students collect, process & interpret data). This residential course includes lectures, labs and fieldwork at USC and on Santa Catalina Island.

Where:  University of Southern California campus and Santa Catalina Island, CA
When:  June 14 – July 2, 2020
Who:  Undergraduates from 2 or 4-year colleges
Cost:  FREE, including travel, plus modest stipend
How to apply: https://www.darkenergybiosphere.org/education-diversity/for-undergraduates/gem-course/

Note:  First generation college, women, and under-represented students encouraged to apply

Application Deadline:  March 25, 2020 at 5:00pm PDT

For questions and comments, contact Gwen Noda at gnoda@usc.edu.

C-DEBI seeks nominations for three speakers for the 2020 program. C-DEBI is continuing the Networked Speaker Series (begun in Fall 2011) as a means to enhance communication and the exchange of ideas among our spatially distributed community. Potential speakers can be nominated by colleagues, mentors, or those mentored by C-DEBI participants; they can also self nominate. Selected C-DEBI Networked Speakers will make a presentation online, using video conferencing tools, with assistance from the C-DEBI main office at USC. Nominated C-DEBI Networked Speakers should be capable of combining compelling visual materials with the ability to communicate effectively to a broad audience. We are particularly enthusiastic about giving young researchers a chance to present work to the C-DEBI community. Being selected to be a C-DEBI Networked Speaker is an honor.

For more information about the Speaker Series and nomination request, please see: https://www.darkenergybiosphere.org/outputs-resources/networked-speaker-series/.

With Dr. James Bradley, Queen Mary University of London on “The power of microbial life in marine sediments.” Abstract: Marine sediments harbor more than half of all microbial cells in the ocean, many of which have been shown to survive for millennia – calling into question the limit for life. The energy turnover, i.e. power, of subseafloor microorganisms sets a limit on gene expression, mutation rates, and the survival of rare and novel taxa. However outside of measurements, laboratory experiments and modelling from specific sites, the power of subsurface life is virtually unknown. Here, we simultaneously quantify the distribution, rate and thermodynamic properties of particulate organic carbon degradation, as well as the global distribution of cells, and electron acceptors. Based on these factors, we estimate cell-specific power utilization in all Quaternary sediments. We report extreme and widespread energy-limitation in subseafloor sediments: >80% of cells subsist at powers that are less than the lowest energy flux calculated for any microbial habitat previously. Furthermore, we find global delineation of major subsurface metabolic zones, with stepwise decreases in per-cell power utilization following the redox state of the sediment. We assert that sediments should be considered as critical to understanding the cell-specific minimum power requirement for survival, as well as to predict the habitable boundaries of life on Earth.

Missed the last seminar with Dr. Jessica Labonté on “You are what you eat: a geochemical and microbial study of a 3000-year old stratigraphic sediment succession”? Watch it on YouTube.

Message from the Director:

We hope the new semester is treating you well, and we also want to congratulate these C-DEBIers who have started new positions: Jackie Goordial (Postdoctoral Fellow at Lamont-Doherty Earth Observatory, Columbia University), Cara Magnabosco (Assistant Professor at ETH Zurich (Swiss Federal Institute of Technology in Zurich)), Gus Ramirez (Postdoctoral Researcher at the University of North Carolina, Chapel Hill), Stephanie Schroeder (STEM Director at Carleton College), Elizabeth Trembath-Reichert (Assistant Professor at Arizona State University), and Katrina Twing (Assistant Professor at Tennessee Tech University). We also congratulate C-DEBI Senior Scientist Beth Orcutt (Bigelow Laboratory for Ocean Sciences) to be awarded the 2019 Asahiko Taira International Scientific Ocean Drilling Research Prize “for outstanding transdisciplinary research accomplishment in ocean drilling” at the 2019 AGU Fall Meeting Honors Ceremony (11 December in San Francisco).

And don’t forget we have two more Networked Speaker Series talks coming up this year! This Thursday, Dr. Jessica Labonté (Texas A&M Galveston) presents “You are what you eat: a geochemical and microbial study of a 3000-year old stratigraphic sediment succession” at 12:30PM Pacific Time. The series ends with  Dr. James Bradley (Queen Mary University of London) on November 7 with “The power of microbial life in marine sediments.” Talks from Dr. Jeanine Ash (Rice University) and Taylor Royalty (University of Tennessee) earlier this year are archived on the NSS website.

Cheers,

Jan Amend
C-DEBI Director

With Dr. Jessica Labonté, Texas A&M Galveston on “You are what you eat: a geochemical and microbial study of a 3000-year old stratigraphic sediment succession.” Abstract: Microbes make up the majority of the biomass in sediment, where they play a role in cycling organic carbon and regulate the fluctuation of organic matter. In anoxic sediment, the relationships between geochemical gradients, genomic potential, and virus-host interactions remain understudied and poorly understood. I will present the results of our study of stratified sediments from anoxic sinkhole (Blackwood Sinkhole, Bahamas), where we analyzed the pore water chemistry analysis (nutrients, carbon, nitrogen), microbial community composition (16S rRNA gebe and metagenomics), and virus-host interactions. Through the characterization of the relationships of microbes between each other and with their environment, we aim to identify the role organic and inorganic matter availability plays in shaping viral and prokaryotic communities, as well as how microbial communities shape their environment. Missed the last seminar with Taylor Royalty on “Quantitatively partitioning microbial genomic traits among taxonomic ranks: implications for subsurface microbial communities?” Watch it on YouTube.

Message from the Director:

Science Magazine’s May 23 Working Life features the brave personal account of Stephanie Schroeder, C-DEBI’s Education Director, on being open with her diagnosis and how it’s changed her own identity with and advocacy for inclusion. Illustration by Robert Neubecker (neubecker.com).

Dear C-DEBI,

Stephanie Schroeder, our Education Director, was diagnosed with multiple sclerosis several years ago. In a recent article in Science Magazine’s Working Life, she opened up about the diagnosis, her subsequent struggles, and the decision to leave high-stress Los Angeles for Minneapolis. She provides a brave and honest account of how going public with her MS has made her a better advocate for members of marginalized groups. Stephanie has been part of C-DEBI since 2012, developing our signature education, outreach and diversity programs, including the Community College Cultivation Cohort (C4) REU, the Global Environmental Microbiology (GEM) course, various teacher training seminars, professional development workshops and more. We are thrilled that Stephanie continues to work passionately for our program participants as she balances her personal health with her professional goals.

Cheers,

Jan Amend
C-DEBI Director

Janice McDonnell (Science Agent, Department of Youth Development, Rutgers University) leads the next C-DEBI Professional Development Webinar on “How to Use the Broader Impact Wizard: A Tool to Help Advance the Impact of Research in Society.” The access URL for the webinar is http://usccollege.adobeconnect.com/cdebiremote/. Missed the last Professional Development Webinar on “Broadening your thinking and your impact: Tips on how to develop effective outreach programs” with Pete Girguis (Harvard)? Watch it on YouTube.

Don’t miss the first of the 2019 online seminars with Dr. Jeanine Ash (Rice University) on “Making and Breaking Molecules.” Abstract: Gases like molecular oxygen and methane are fundamentally significant to Earth’s habitability and the evolution of life.  The concentration of these gases in our atmosphere are the result of constant interplay between the biological and geological process that create and consume them. My work focuses on the enzyme-level processes that make and break these molecules, and how recent advances in isotope ratio mass spectrometry can provide new tools for tracing these process at the global level.  In this talk I’ll introduce the concept of multiply-substituted isotopologues (commonly called “clumped” isotopes), and share case studies that show how these tools can be used to illuminate deep biosphere processes.

Message from the Director:

Seafloor borehole observatories (CORKs) at Juan de Fuca Ridge flank to be revisited this month to make further discoveries about the activity of life in the deep crustal biosphere. Photo courtesy of 2013 Juan de Fuca Ridge flank cruise AT26-03 with ROV Jason (WHOI, chief scientist Andrew Fisher of University of California, Santa Cruz, NSF).

The month of May finds several C-DEBI scientists returning to the Juan de Fuca Ridge flank to examine microbes in the crustal subsurface. Led by C-DEBI Senior Scientist Beth Orcutt, the NSF-funded “Slow Life in the Fast Lane” cruise has a primary objective to measure microbial activity in this environment. Orcutt’s group will be conducting stable isotope incubations in situ and shipboard to measure various microbial metabolisms in this ecosystem, and comparing these to shore-based potential rate measurements. Leveraging these experiments, Orcutt and colleagues will also be applying new cell sorting techniques developed by collaborator Ramunas Stepanauskas to identify active microbial groups in this ecosystem as well as in the overlying water column, with leveraged funding from NASA and NSF. C-DEBI community members Stephanie Carr, Olivia Nigro, and Michael Rappé will also be on the cruise with support from NSF to lead parallel guided cultivation, ecogenomic and viral studies on the crustal fluids in collaboration with an international team of cultivation and thermophilic spore experts. The cruise will take place May 15-28 aboard the RV Atlantis with ROV Jason. Follow along on Twitter at #SlowLifeFastLane.

We also congratulate C-DEBIers who have recently been awarded, promoted or are starting new positions: James Bradley (Assistant Professor at Queen Mary University of London); Jen Glass (Associate Professor at Georgia Institute of Technology); and Everett Shock (Arizona State University), honored with the 2019 Geochemistry Division Medal by the American Chemical Society.

Cheers,

Jan Amend
C-DEBI Director

Message from the Director:

This is Alvin, a submarine operated by the Woods Hole Oceanographic Institution. It’s capable of reaching depths of 4,500 meters and carries two scientists and one pilot on each dive. Photo courtesy of Luis Lamar, WHOI.

Dear C-DEBI,

C-DEBIer Jason Sylvan (Texas A&M University) is leading a research cruise to study how microbiology, mineralogy, and geology change on hydrothermal vent sulfides right after they stop venting. #Hot2ColdVents, funded by the National Science Foundation, will go to 9˚50”N on the East Pacific Rise during March 25-April 24, 2019 and use Alvin to sample active hydrothermal sulfides and then leave them exposed on the seafloor for one week and one year to follow the changes post-venting. Learn more at the project website and follow the cruise blog.

Cheers,

Jan Amend
C-DEBI Director

Know someone who can share their knowledge of essential skills not learned in graduate school, like developing a syllabus, how to choose what professional service committees to serve on or how to transition to a career in industry? C-DEBI seeks nominations for its Professional Development Webinar series. In addition to providing training in state-of-the-art technologies and instrumentation for graduate students and beyond, we emphasize professional development training targeting skills needed both in and out of academia. These live interactive webinars provide transferable skills for all early career scientists and will be archived on the website for those unable to “attend” the live events. Potential speakers can be nominated by colleagues, mentors, or those mentored by C-DEBI participants; they can also self-nominate. Selected C-DEBI Professional Development Speakers will make a presentation online, using video conferencing tools, with assistance from the C-DEBI main office at USC. Nominated C-DEBI Professional Development Speakers should be capable of combining compelling visual materials with the ability to communicate effectively to a broad audience. Please send nominee name, contact info/description, and subject topic to Education, Outreach, & Diversity Managing Director, Stephanie Schroeder slschroe@usc.edu.

Pete Girguis (Professor of Organismic and Evolutionary Biology, Harvard University) leads the next C-DEBI Professional Development Webinar on “Broadening your thinking and your impact: Tips on how to develop effective outreach programs.” The access URL for the webinar is http://usccollege.adobeconnect.com/cdebiremote/. Missed the last Professional Development Webinar on “Lessons Learned: Adventures in Online Teaching and Trying to Balance Research & Teaching” with Jason Sylvan (Texas A&M)? Watch it on YouTube.

C-DEBI seeks nominations for three speakers for the 2019 program. C-DEBI is continuing the Networked Speaker Series (begun in Fall 2011) as a means to enhance communication and the exchange of ideas among our spatially distributed community. Potential speakers can be nominated by colleagues, mentors, or those mentored by C-DEBI participants; they can also self nominate. Selected C-DEBI Networked Speakers will make a presentation online, using video conferencing tools, with assistance from the C-DEBI main office at USC. Nominated C-DEBI Networked Speakers should be capable of combining compelling visual materials with the ability to communicate effectively to a broad audience. We are particularly enthusiastic about giving young researchers a chance to present work to the C-DEBI community. Being selected to be a C-DEBI Networked Speaker is an honor.

CC-RISE is an eight-week, paid, summer research internship program for community college students run by the Center for Dark Energy Biosphere Investigations. Students will gain firsthand exposure to the scientific process by working in a faculty-led research lab at the Woods Hole Oceanographic Institution in Woods Hole, MA. In addition to research, students will participate in activities focusing on how to transition from a two-year college to a university and information on graduate school. At the end of the program, students will present their results to an audience of peers and mentors. Applications are due March 29, 2019.

Message from the Director:

Dear C-DEBI,

Congrats to the Dorado octopus team including Geoff Wheat and Anne Hartwell for capturing the photo of octopus moms above and making NSF’s “Most popular stories of 2018”!

I also encourage you to apply to the “NEXT: Scientific Ocean Drilling Beyond 2023” workshop for the future of scientific ocean drilling to be held in Denver, Colorado, USA on May 6-7, 2019. The NEXT workshop will convene approximately 120 IODP community members to develop the US plan for continued scientific ocean drilling without a hiatus at the end of the current program ending in 2023 and continue planning to replace the aging JOIDES Resolution with a modernized, more capable non-riser drilling vessel to help accommodate the transition to a long-term future in scientific ocean drilling. The deadline to apply is 2/15/19.

Cheers,

Jan Amend
C-DEBI Director

Jason Sylvan, (Assistant Professor, Texas A&M) leads the next C-DEBI Professional Development Webinar on “Lessons Learned: Adventures in Online Teaching and Trying to Balance Research & Teaching.” The access URL for the webinar is http://usccollege.adobeconnect.com/cdebiremote/. Missed the most recent C-DEBI Professional Development Webinar on “Scientific Editing as a Career” with Delphine Defforey (Nature Communications)? Watch it on YouTube.

AGU Fellow and C-DEBI Co-I Andy Fisher flanked by C-DEBI Co-Is Julie Huber and Geoff Wheat.

Message from the Director:

Congratulations again to C-DEBI co-Investigator Andy Fisher who was honored as an AGU Fellow last week! Hope those that attended the American Geophysical Union Fall Meeting in DC had a terrific week of deep biosphere sessions!

Cheers,

Jan Amend
C-DEBI Director

Use LinkedIn for professional networking or job discovery? Add our job announcements and other relevant news to your feed by “following” C-DEBI’s company page, and link your profile via the Work Experience section (e.g., “Postdoctoral Fellow at C-DEBI: Center for Dark Energy Biosphere Investigations”).

Delphine Defforey, (Associate Editor at Nature Communications) leads the next C-DEBI Professional Development Webinar on “Scientific editing as a career.” The access URL for the webinar is http://usccollege.adobeconnect.com/cdebiremote/. Missed the most recent C-DEBI Professional Development Webinar on “Work-life Balance is Essential and also it can’t Possibly Exist” with Drew Steen (UTK)? Watch it on YouTube.

Message from the Director:

We are enjoying great talks, posters, company and weather at our Annual Meeting in Marina, CA discussing current C-DEBI activities with our active research and education participants.

Cheers,

Jan Amend
C-DEBI Director

Message from the Director:

Let me begin with sincere congratulations to C-DEBIers Jennifer Biddle (University of Delaware) awarded the UD College of Earth, Ocean, and Environment’s Outstanding Faculty Mentor Award and Elizabeth Trembath-Reichert (Woods Hole Oceanographic Institution) awarded a 2018 L’Oreal For Women in Science Fellowship.

On a policy front, the NSF has recently announced new measures to protect the research community from harassment. Like NSF, C-DEBI is committed to promoting safe, productive research and education environments for current and future scientists and engineers and will not tolerate harassment, including sexual or sexual assault within our community. C-DEBI’s Ethics Policy also maintains avenues for potential ethical misconduct resolution for members of the C-DEBI community.

Finally, all good things must come to an end. C-DEBI is an NSF Science and Technology Center, and we have entered year 9 (of 10). In the final 18 months, NSF funding for all STCs scales back substantially, and a number of changes at C-DEBI must consequently occur in the phase down. 2018 represented the last round of the Research Grants and Fellowships programs; we now move towards synthesis activities (and continue to support community workshops). We must also eliminate a number of our Education, Outreach, and Diversity programs, but we are developing plans for sustaining some of these with outside support. 2018 also marks the end of CC-RISE at UCSC, Community College Instructor Workshops, Teacher Small Grants, and the USC SeaGrant Summer Marine Science Camp; 2019 will see the final installments of CC-RISE at WHOI, the GEM course, and GGURE. The community college C4 REU has been hugely successful, and we have submitted a renewal proposal to the NSF for 2020. As we approach the end of NSF-funding, we continue to strategize on how to maintain C-DEBI and our community in its next phase. Suggestions and creative ideas are more than welcome!

Cheers,

Jan Amend
C-DEBI Director

Join us online for our third Networked Speaker Series seminar of of the 2018 season, featuring Dr. Jackie Goordial (Bigelow Laboratory for Ocean Sciences) on “Microbial activity and ecology through sorted cell -omics of Mid-Atlantic ridge oceanic crust and sediments.” Missed the last seminar with Dr. Alma Parada (Stanford University) on “Evaluating the diversity and distribution of novel microbes across physical and geochemical gradients in deep-sea sediments”? Watch it on YouTube.

Join us online for our second Networked Speaker Series seminar of of the 2018 season, featuring Dr. Nagissa Mahmoudi (McGill University) on “Uncovering microbial species-specific effects on organic matter transformation in marine sediments.” Missed the last seminar with Dr. Alma Parada (Stanford University) on “Evaluating the diversity and distribution of novel microbes across physical and geochemical gradients in deep-sea sediments”? Watch it on YouTube.

Message from the Director:

Hope you are having a good start to your semester – we especially wish the same to C-DEBIers who have been promoted or are starting new positions: Karen Lloyd (Associate Professor at University of Tennessee Knoxville), Nagissa Mahmoudi (Assistant Professor at McGill University), and Alberto Robador (Research Assistant Professor at University of Southern California).

And a sincere congratulations to C-DEBIers being recognized for their scientific excellence and more this year: Victoria Orphan (Caltech) recipient of the NOMIS Distinguished Scientist and Scholar Award, Beth Orcutt (Bigelow) to receive the Geological Society of America Geobiology & Geomicrobiology Division Post-Tenure Award, and Andy Fisher (UCSC) and Adina Paytan (UCSC) to be named American Geophysical Union Fellows.  Please share your personal kudos if you will also be attending the GSA Annual Meeting in Indiana in November and the AGU Fall Meeting in DC in December.

Cheers and good luck to all submitting NSF proposals due today!

Jan Amend
C-DEBI Director

The Genomics and Geobiology Undergraduate Research Experience (GGURE) is a research internship program for USC sophomores, juniors, and seniors majoring in the life sciences, earth and marine sciences, computational sciences, and engineering. There is both a part-time program during the academic year and a full-time program over 10 weeks during the summer break at the University of Southern California. The GGURE program offers USC undergraduates the opportunity to participate actively in a research group, with either an experimental or computational focus, and perform original research under the direct supervision of a faculty mentor. We will begin reviewing applications on Monday, August 20, 2018 but will continue to review applications until all positions are filled.

Drew Steen (C-DEBI Assistant Professor of Environmental Geology, University of Tennessee) leads the next C-DEBI Professional Development Webinar on “Work-life Balance is Essential and also it can’t Possibly Exist.” The access URL for the webinar is http://usccollege.adobeconnect.com/cdebiremote/. Missed the most recent C-DEBI Professional Development Webinar on “What I wish I knew before I knew it: Surviving the early years of tenure-track faculty” with Brandi Kiel Reese (TAMU)? Watch it on YouTube.

You are cordially invited to the Center for Dark Energy Biosphere Investigations’ Community College Cultivation Cohort (C4) summer presentation symposium. Students from the C-DEBI NSF REU: C4 program will share their results from the summer. The C4 students will also present their findings at the Undergraduate Research Poster Symposium on August 10. Please see the flyer for details. Students-friends & family are welcome. Mentors/PIs-please share with other members of your lab. Light refreshments will be served at both events.

Brandi Kiel Reese (Assistant Professor, TAMU-CC) leads the next C-DEBI Professional Development Webinar on “What I wish I knew before I knew it: Surviving the early years of tenure-track faculty.” The access URL for the webinar is http://usccollege.adobeconnect.com/cdebiremote/. Missed the most recent C-DEBI Professional Development Webinar on “Sharing Data: The Joys of Open Science” with Ben Tully (C-DEBI Bioinformatic Specialist)? Watch it on YouTube.

Our 2018 Networked Speaker Series speakers have been selected! These early career investigators were nominated by members of the community for their exciting research and effective communication, so mark your calendars! The intent of these half-hour talks is to connect all of us interested “deeply” or broadly in the deep biosphere.

• NSS #18: Dr. Alma Parada, Stanford University
  Evaluating the diversity and distribution of novel microbes across physical and geochemical gradients in deep-sea sediments
  May 31, 2018, live online, 9:30AM HAST / 12:30PM PDT / 3:30PM EDT
• NSS #19: Dr. Nagissa Mahmoudi, McGill University starting August 2018
  September 20, 2018, live online, 9:30AM HAST / 12:30PM PDT / 3:30PM EDT
• NSS #20: Dr. Jackie Goordial, Bigelow Laboratory for Ocean Sciences
  September 27, 2018, live online, 9:30AM Hawaii Time / 12:30PM PST / 3:30PM EST
• NSS #21: Dr. Rosa León Zayas, Willamette University
  October 18, 2018, live online, 9:30AM Hawaii Time / 12:30PM PST / 3:30PM EST

Detailed insight into the microbiome of a system can shape our understanding of it, but the learning curve for incorporating computationally intensive tools can be very high! Join instructor Dr. Benjamin Tully, C-DEBI Bioinformatic Specialist, for an upcoming bioinformatics workshop at the University of Southern California, June 21-22, 2018. All expenses are covered courtesy of the NSF STCs C-DEBI, EBICS, and BEACON. Topics include: Unix command line; Illumina sequence quality control; Metagenomic experimental design; Sequence Assembly; Metageomic binning; Functional Annotation; and Phylogenetic analysis. Note: participation requires a laptop with 40 GB of hard drive space. To apply: email tully.bj@gmail.com by May 28, 2018 – be sure to include your home institution, your home STC, and what you hope to get out of the workshop. All levels are welcome. There is a 15 participant maximum, so apply soon!

Message from the Director:

In celebration of the 30th anniversary of the NSF Science and Technology Center Program, Discover magazine featured C-DEBI in their image gallery of some of the STCs’ groundbreaking work!

Please mark your calendars for this month’s Professional Development Webinar “Sharing Data: The Joys of Open Science” by Ben Tully (C-DEBI Bioinformatic Specialist, USC), April 25th, 12-1pm PST.

And congratulations to the proponents of proposals selected for funding in our 2017 December call for research grants and fellowships. Stay tuned on our funded projects webpage for their exciting work!

• Graduate Fellowship: Taylor Royalty (Advisor: Drew Steen, University of Tennessee Knoxville)
  Characterization of subsurface extracellular enzymes and the organisms that produce them using metatranscriptomics and bottom-up metaproteomics
  
• Graduate Fellowship: Clarisse Sullivan (Advisor: Mike Rappe, University of Hawaii)
  Population genomics of Nitrospirae bacteria inhabiting deep subseafloor fluids of the Juan de Fuca Ridge flank
  
• Postdoctoral Fellowship: Sarah Hu (Advisor: Julie Huber, Woods Hole Oceanographic Institution)
  Probing subseafloor microbial interactions via hydrothermal vent fluids: A focus on protists
• Postdoctoral Fellowship: Claire McKinley (Advisor: Evan Solomon, University of Washington)
  Evaluating the extent of microbial Fe-reduction and its role in the global methane cycle
  
• Research Grant: Annie Rowe, University of Cincinnati
  Uncovering novel mechanisms of extracellular electron uptake in subsurface-relevant marine bacterial isolates

Cheers,

Jan Amend
C-DEBI Director

Missed the most recent C-DEBI Professional Development Webinar on “Sharing Data: The Joys of Open Science” with Ben Tully (C-DEBI Bioinformatic Specialist)? Watch it on YouTube.

Missed the last webinar on “Surviving (and Maybe Even Thriving!) in a Soft Money Position” with Julie Huber (C-DEBI Associate Director, Associate Scientist, WHOI)? Watch it on YouTube.

Congratulations to C-DEBI scientists Elizabeth Trembath-Reichert and Victoria Orphan for the selection of their PNAS paper, Methyl-compound use and slow growth characterize microbial life in 2-km-deep subseafloor coal and shale beds (C-DEBI Contribution 389), for the 2017 Cozzarelli Prize. The annual award acknowledges papers that reflect scientific excellence and originality and is given annually to six papers published in PNAS.

Message from the Director:

At the end of January, we had our annual site review by NSF and the external panel, and thank all involved including our strong group of undergraduates, graduate students and postdocs who continue to be one of the great successes of C-DEBI.

Congratulations to C-DEBIers who have started new positions this spring semester: Olivia Nigro (Assistant Professor of Biology at Hawaii Pacific University) and Annie Rowe (Assistant Professor of Biological Sciences at University of Cincinnati).

And don’t forget to mark your calendars for this month’s Professional Development Webinar “Surviving (and Maybe Even Thriving!) in a Soft Money Position” by Julie Huber, C-DEBI Associate Director, Associate Scientist, WHOI – February 28th, 12-1pm PST.

Cheers,

Jan Amend
C-DEBI Director

CC-RISE is an eight-week, paid, summer research internship program for community college students run by the Center for Dark Energy Biosphere Investigations. Students will gain firsthand exposure to the scientific process by working in a faculty-led research lab at the University of California Santa Cruz or at the Woods Hole Oceanographic Institution in Woods Hole, MA. In addition to research, students will participate in activities focusing on how to transition from a two-year college to a university and information on graduate school. At the end of the program, students will present their results to an audience of peers and mentors. Applications are due March 31, 2018.

The Genomics and Geobiology Undergraduate Research Experience (GGURE) is a research internship program for USC sophomores, juniors, and seniors majoring in the life sciences, earth and marine sciences, computational sciences, and engineering. There is both a part-time program during the academic year and a full-time program over 10 weeks during the summer break at the University of Southern California. The GGURE program offers USC undergraduates the opportunity to participate actively in a research group, with either an experimental or computational focus, and perform original research under the direct supervision of a faculty mentor. We will begin reviewing applications on Tuesday, January 2, 2018 but will continue to review applications until all positions are filled.

Message from the Director:

Proposals for C-DEBI Research Grants and Fellowships are due today! If you miss these annual calls, don’t forget we also support C-DEBI Community Workshops and Research Exchanges in a year-round call.

NSF Geoscience is again seeking input on exciting research to call out for support in their next report. Please comment on your perspective of deep biosphere research as an area to continue to fund by 2/1/18.

At last month’s C-DEBI Annual Meeting, our presently-funded research and education community met to discuss our current activities. The meeting was preceded by a graduate student and postdoctoral professional development workshop “Key steps to landing a job and what to do once you’ve been offered the position.” See the agenda.

Another season of our Networked Speaker Series is over and we thank the presenters for their great talks connecting all of us interested “deeply” or broadly in the deep biosphere (watch the archived talks online). Nominate an early career investigator doing exciting research with effective communication for next season’s series!

Going to the 2017 AGU Fall meeting this month? Join DCO and C-DEBI for a poster swarm of Session B11G “Unearthing the Metabolic Potential of Microorganisms in the Deep Subsurface Biosphere II Posters” on Monday December 11. Gather at poster B11G-1729 at 10AM to hear short presentations of posters in the session followed by questions and discussion. See additional sessions of interest. While you are at the meeting, share your photos, scientific ponderings, and new found knowledge with us on Twitter! Please tag any NSF-funded C-DEBI research with #NSFfunded, @NSF_GEO and @deepbiosphere. Both C-DEBI and NSF are prepared to share your Tweets!”

Cheers,

Jan Amend
C-DEBI Director

C-DEBI seeks nominations for three speakers for the 2018 program. C-DEBI is continuing the Networked Speaker Series (begun in Fall 2011) as a means to enhance communication and the exchange of ideas among our spatially distributed community. Potential speakers can be nominated by colleagues, mentors, or those mentored by C-DEBI participants; they can also self nominate. Selected C-DEBI Networked Speakers will make a presentation online, using video conferencing tools, with assistance from the C-DEBI main office at USC. Nominated C-DEBI Networked Speakers should be capable of combining compelling visual materials with the ability to communicate effectively to a broad audience. We are particularly enthusiastic about giving young researchers a chance to present work to the C-DEBI community. Being selected to be a C-DEBI Networked Speaker is an honor.

Message from the Director:

That’s a wrap! After almost 3 weeks on site at North Pond, a diverse team of microbiologists, geochemists, hydrogeologists, and virologists are leaving station and heading to Barbados! We look forward to learning what they’ve discovered!

The special issue of Frontiers in Microbiology, Recent Advances in Geomicrobiology of the Ocean Crust, is now available as an “ebook.” These twenty-two papers that came out earlier this year in tribute to the late Dr. Katrina J. Edwards brings together recent discoveries of the microbial presence, diversity and activity in these environments, with analysis of the implications for global systems.

Cheers,

Jan Amend
C-DEBI Director

Dr. Emily Estes (University of Delaware) will give the next Networked Speaker Series Seminar on “Organic carbon utilization and preservation in a carbon desert.” Abstract: Organic carbon (OC) preserved in marine sediments acts as a reduced carbon sink that balances the global carbon cycle. Understanding the biogeochemical mechanisms underpinning the balance between OC preservation and degradation is thus critical both to quantifying this carbon reservoir and to estimating the extent of life in the deep biosphere. This work examines the content and composition of OC in oxic pelagic sediments from the North Atlantic and South Pacific gyres in order to evaluate preservation mechanisms operating on million-year time scales and to gage heterotrophic activity in these OC-limited environments. We utilize a combination of elemental analysis/isotope ratio mass spectrometry and novel synchrotron-based X-ray absorption spectroscopy. These techniques interrogate the entire particulate organic carbon pool in contrast to more commonly applied techniques that require chemical extractions or demineralization. OC and nitrogen concentrations decrease exponentially from the sediment-water interface to values <0.1% in the deep subsurface and, to a first order, scale with sediment oxygenation. In the deep subsurface, however, molecular recalcitrance becomes more important than oxygen exposure time in protecting OC against remineralization. Deep OC consists of primarily amide and carboxylic carbon in a scaffolding of aliphatic and O-alkyl moieties, corroborating the extremely low C/N values observed. These findings suggest that microbes in oxic pelagic sediments are carbon-limited and may preferentially remove carbon relative to nitrogen from the organic matter pool.

The NSF Science and Technology Center for Dark Energy Biosphere Investigations (C-DEBI) invites proposals for 1-year research projects (in the anticipated range of $50,000-$80,000) and 1-2 year graduate student and postdoctoral fellowships that will significantly advance C-DEBI’s central research agenda: to investigate the subseafloor biosphere deep in marine sediment and oceanic crust, and to conduct multi-disciplinary studies to develop an integrated understanding of subseafloor microbial life at the molecular, cellular, and ecosystem scales. C-DEBI’s research agenda balances exploration-based discovery, hypothesis testing, data integration and synthesis, and systems-based modeling. C-DEBI welcomes proposals from applicants who would enhance diversity in C-DEBI and STEM fields. This request for proposals is open to all interested researchers at US institutions able to receive NSF funding as a subaward. The deadline for this call is December 1, 2017.

Message from the Director:

Our annual call for research and fellowship proposals is posted! We continue to support research grants and graduate student and postdoctoral fellowships that will significantly advance C-DEBI’s central research agenda to investigate the subseafloor biosphere deep in marine sediment and oceanic crust, including on “expeditions of opportunity.” C-DEBI welcomes proposals from applicants who would enhance diversity in C-DEBI and STEM fields. The deadline for this call is December 1, 2017. Note, there is no call for education grants this year. I look forward to continued, strong engagement by the community through our many C-DEBI programs and activities.

As the culminating program for the North Pond field program – a major field site within the C-DEBI portfolio – a team of scientists is heading back to the subseafloor “CORK” observatory network in October to assess the deep biosphere living in young, cool, and oxic basaltic oceanic crust. This observatory network was installed in 2011 during IODP Expedition 336 led by former C-DEBI Director Katrina Edwards. C-DEBI scientists led by Executive Committee member Dr. Geoff Wheat will be visiting the observatories with the ROV Jason to collect pristine subsurface fluid samples and finally recover the sensors and incubation experiments that have been cooking in the subsurface for the past 6 years. This return mission is funded by the National Science Foundation, with add-on funding for fluid sampling to look at microbe-carbon and virus interactions. Cruise participants will also be running a ship-to-shore outreach program. Follow #NorthPond2017 on Twitter for the latest updates.

In this summer’s Global Environmental Microbiology (GEM) course and Community College Cultivation Cohort (C4) REU, we had another enthusiastic and bright class of undergraduate students that we will be introducing you to in our newsletters, sharing their stories and aspirations. We are proud to have been a step in their scientific pathway.  Please keep your eye out for their spotlights!

Cheers,

Jan Amend
C-DEBI Director

Andrew Fisher (C-DEBI Co-PI, University of California Santa Cruz) leads the next C-DEBI Professional Development Webinar on “Speaking as a Scientist with Press, Politicians, and the Public.” The access URL for the webinar is http://usccollege.adobeconnect.com/cdebiremote/. Missed the last webinar on “How to Negotiate in Academia”? Watch it on YouTube.

The NSF Science and Technology Center for Dark Energy Biosphere Investigations (C-DEBI) invites proposals for 1-year research projects (in the anticipated range of $50,000-$80,000) and 1-2 year graduate student and postdoctoral fellowships that will significantly advance C-DEBI’s central research agenda: to investigate the subseafloor biosphere deep in marine sediment and oceanic crust, and to conduct multi-disciplinary studies to develop an integrated understanding of subseafloor microbial life at the molecular, cellular, and ecosystem scales. C-DEBI’s research agenda balances exploration-based discovery, hypothesis testing, data integration and synthesis, and systems-based modeling. C-DEBI research support is provided to “expeditions of opportunity”, and we’ve created a webpage listing potential options for participation. We welcome you to provide information about other expeditions of opportunity to share with the C-DEBI community! Help us further our mission to explore life beneath the seafloor and make transformative discoveries that advance science, benefit society, and inspire people of all ages and origins. C-DEBI welcomes proposals from applicants who would enhance diversity in C-DEBI and STEM fields. This request for proposals is open to all interested researchers at US institutions able to receive NSF funding as a subaward. The next deadline for these annual calls is December 1, 2017.

Message from the Director:

After an exciting 10-year run, the Center for Geomicrobiology at Aarhus University in Denmark officially closes its doors at the end of this month. Under the leadership of Bo Barker Jørgensen, this center made exciting discoveries on microbial life in the seabed, including in the sediment sulfur cycle, life at the energetic limits, and electromicrobiology, to name but a few. The center may be sunsetting, but we look forward to many future collaborations with our friends from across the Atlantic.

And remember to tune in to our webinars this season! Emily Estes is our next Networked Speaker on November 2 ( Organic carbon utilization and preservation in a carbon desert), and Andy Fisher is our next Professional Development speaker on October 24 (Title TBD). If you missed the latest ones, please check out the fantastic talks by Gus Ramirez ( Microbial Neter-Khertet: Life and death post-entombment) and Karen Lloyd (How to Negotiate in Academia) archived on the website.

Finally, congratulations to Heather Fullerton starting this fall as an Assistant Professor in Biology at the College of Charleston. We are enthusiastic for the group of C-DEBIers starting new positions this fall, and look forward to continuing to share their and others’ good news.

Cheers,

Jan Amend
C-DEBI Director

The K-16 Educator Small Grants program supports K-16 teachers who have attended a C-DEBI educator training program and have incorporated C-DEBI content into their classrooms.  These awards up to $2500 support items including but not limited to the following: funds for student field trips, classroom supplies, travel for presenting C-DEBI curriculum at educator meetings, or additional professional development directly related to C-DEBI research.  Proposals for funding should indicate how C-DEBI research content is being translated into the classroom and how the proposed activities connect to that content. Applications are due October 2, 2017.

Hope you are having a good start to your semester – we especially wish the same to C-DEBIers who we know have started new positions: Rika Anderson (Assistant Professor at Carleton College), Stephanie Carr (Assistant Professor at Hartwick College), Kat Dawson (Assistant Professor at Rutgers University), Caroline Fortunato (Assistant Professor at Wilkes University), Anna Kaster (Professor at Karlsruhe Institute of Technology), Ileana Perez-Rodriguez (Assistant Professor at the University of Pennsylvania), Mark Torres (Assistant Professor at Rice University), Rosa Léon-Zayas (Assistant Professor at Willamette University) and Senior Scientist Steve Finkel (College Dean of Graduate and Professional Education at the University of Southern California).

August 24, 11am PT:Karen G. Lloyd (University of Tennessee) leads the next C-DEBI Professional Development Webinar on “How to Negotiate in Academia,” covering why negotiation is essential, tips for how to do so successfully and what to expect from post-doc and assistant professorship job negotiations.

September 7, 12:30pm PT: Dr. Gustavo Ramírez (University of Rhode Island) will give the next Networked Speaker Series Seminar on “Microbial Neter-Khertet: Life and death post-entombment.” Abstract: Deep ocean sediment is a diffusion-limited environment where microbial inhabitants persist despite extreme temporal, physical and nutritional isolation from the ocean above. Burial time increases with sediment depth and, unsurprisingly, community richness, diversity, cell abundance and metabolic activity drop significantly with sediment age, implying both a steep selection curve and concomitant mass death. The extent to which benthic necromass (fragments of cadaverous cells), specifically extracellular DNA, a molecular fossil, may affect environmental sequencing surveys is a critical question that has received little attention. Reasons for this neglect are i) DNA is generally believed to have a short molecular half-life and ii) extracellular DNA represents dissolved C, N and P which should be readily metabolized by active microbes. The scarcity of methods for assessing microbial viability in complex environmental samples further confounds this issue. I interrogated Arctic and Pacific sediments for the presence of detrital DNA using Propidium Monoazide, a photo-active DNA intercalating dye that cannot penetrate intact prokaryotic membranes. This approach employs membrane integrity, a prerequisite for chemiosmotic potential and ATP production, as a viability metric. I detected statistically significant extracellular 16S rRNA gene loads in shallow sediment horizons, but not deep horizons. Measures of Alpha- and Beta-diversity for intra-and total-16rRNA gene pools are somewhat variable. Diversity trends are generally similar for both DNA pools, but noisier at shallow depths.

Message from the Director:

In tribute to the late Dr. Katrina J. Edwards, who pioneered C-DEBI and the study of microbes that “rust the crust”, a special issue of twenty-two papers, Recent Advances in Geomicrobiology of the Ocean Crust, has been published in Frontiers in Microbiology. Editors Beth Orcutt, Jason Sylvan and Cara Santelli are just a few of the many in our community inspired by her achievements in the exploration of the deep biosphere.

And a round of hearty congratulations to our C-DEBIers at (or formerly at) the University of Delaware: Dr. Jen Biddle, Dr. Rosa Leon Zayas and Christopher Petrone. Jen Biddle and her co-investigators have been awarded a prestigious $1 million grant from the W.M. Keck Foundation to explore how environmental factors may affect the genetics of microbes. Rosa Leon Zayas, a former C-DEBI postdoctoral fellow, begins her tenure track position at Willamette University in the Department of Biology this fall. And Chris Petrone’s C-DEBI education grant Project VIDEO, developed with Lisa Tossey, Jen Biddle and Rosa Leon Zayas, has won two national awards for audiovisual communications and electronic media. Congratulations to all of you and the C-DEBIers who contributed to the guest 15 Second Science spots!

Cheers,

Jan Amend
C-DEBI Director

To help preserve deep biosphere methods for use in future projects, the Center strongly encourages you to describe your lab and software-based methods using protocols.io, and to link them to our group page at https://www.protocols.io/groups/center-for-dark-energy-biosphere-investigations. The protocols.io website provides an easy-to-use platform to share reproducible, step-by-step scientific methods. So far, our group has 10 protocols up and we hope to preserve as many methods as possible from the community, including both successful and failed protocols. Please contact Matt Janicak <janicak@usc.edu> if you have any questions about using the site and we hope to see your contributions up soon.

Karen G. Lloyd (University of Tennessee) leads the next C-DEBI Professional Development Webinar on “How to Negotiate in Academia,” covering why negotiation is essential, tips for how to do so successfully and what to expect from post-doc and assistant professorship job negotiations. Missed the last webinar on “Proposal Writing, Management, and Budget Planning”? Watch it on YouTube.

You are invited to join us for our Undergraduate Research Poster Symposium featuring research on coastal ocean processes, subseafloor microbes and more by undergraduates of the USC Wrigley Institute for Environmental Studies Summer REU program and the Center for Dark Energy Biosphere Investigations C4 and GGURE programs. Light refreshments will be served. Please send an email to Gwen Noda gnoda@usc.edu to let us know that you plan to attend. See the flyer for more details.

C-DEBI teamed up with the Consortium for Ocean Leadership’s Marine Geoscience Leadership Symposium (MGLS) for this comprehensive webinar on proposal preparation June 15, 2017. The webinar focused on topics related to preparing research proposals by providing advice on writing, constructing planning timelines, managing a team through the process, and preparing a budget. In addition to the 1 hour 20 minute video, PDFs are available of the presentation slides and a supplemental question answered from the extensive Questions and Discussion at the end of the webinar.

Message from the Director:

Congratulations to Dr. Andy Fisher, C-DEBI Co-Investigator, recognized by the University of California Santa Cruz with the 2016-17 Excellence in Teaching Award (one of seven university-wide).

And good luck to our newest deep biosphere researchers getting started in C-DEBI’s summer Education & Diversity programs! These include our Community College Cultivation Cohort (C4) REU at USC, where community college students cultivate and characterize unknown microbes from the deep; the Community College Research Internship for Scientific Engagment (CC-RISE ) for community college students at WHOI and UCSC; the Geobiology and Genomics Undergraduate Research Experience (GGURE) internship at USC; the undergraduate, field-based Global Environmental Microbiology Course at USC and Wrigley Institute; the Summer Marine Lab Experience for high school students from across the country at Wrigley; and the Seafloor Science ROV day camp for elementary and Jr. High students at several locations in the Monterey Bay area.

Cheers,

Jan Amend
C-DEBI Director

Message from the Director

Our Associate Director, Dr. Julie Huber begins her new position in Marine Chemistry & Geochemistry at the Woods Hole Oceanographic Institution this month, so please update your address books to jhuber@whoi.edu!  A round of congratulations also to Dr. Jen Biddle awarded tenure in the College of Earth, Ocean, and Environment at the University of Delaware and Dr. Laura Lapham awarded tenure at the Chesapeake Biological Laboratory at the University of Maryland Center for Environmental Science. And if you are at this week’s ASM Microbe meeting, please congratulate C-DEBI Senior Scientist Dr. Steve Finkel who will receive the William A. Hinton Research Training Award on June 4 for outstanding contributions toward fostering the research training of underrepresented minorities in microbiology. Steve’s GGURE undergraduate research internship program is one of C-DEBI’s flagship STEM-retention programs.

We are also pleased to share that the International Ocean Discovery Program has just put Guaymas Basin deep drilling led by Dr. Andreas Teske on the agenda for late 2019, so keep your eye out for opportunities to sail on Expedition 385: Guaymas Basic Tectonics and Biosphere!
Cheers,

Jan Amend
C-DEBI Director

Speakers:Donna Blackman (Scripps Institution of Oceanography) and Beth Orcutt (Bigelow Laboratory for Ocean Sciences). For our upcoming C-DEBI Professional Development Webinar, we have teamed up with the Consortium for Ocean Leadership’s Marine Geoscience Leadership Symposium (MGLS) to bring you a comprehensive webinar on proposal preparation. The webinar will focus on topics related to preparing research proposals by providing advice on writing, constructing planning timelines, managing a team through the process, and preparing a budget. Please register to access the webinar link and receive last-minute email reminders!

Congratulations to Dr. Anne Dekas at Stanford University, named one of the 2017 Simons Foundation Early Career Investigators in Marine Microbial Ecology and Evolution.  Dr. Dekas is a C-DEBI scientist who studies the microbiology and biogeochemistry of the deep sea, and with this award, will quantify microbial activity in the deep sea using NanoSIMS.

And please tune in to our next Networked Speaker Series talk on 5/11 by Dr. Andrew Steen at the University of Tennessee, Knoxville presenting “What Heterotrophs Want: Using extracellular enzyme assays to probe the lifestyle of heterotrophic microorganisms in subsurface sediments.”

Message from the Director:

Looking forward to another great Networked Speaker Series talk on 5/11: Dr. Andrew Steen, Assistant Professor at the University of Tennessee, Knoxville presents “What Heterotrophs Want: Using extracellular enzyme assays to probe the lifestyle of heterotrophic microorganisms in subsurface sediments.” The intent of these half-hour talks is to connect all of us interested “deeply” or broadly in the deep biosphere. Note, these early career investigators were nominated by members of the community for their exciting research and effective communication!

If you missed this season’s previous talk, Dr. Annie Rowe: Eating rocks! Investigating microbial energy conservation with microbes that utilize solid mineral electron donors, you can watch it now online.

Cheers,

Jan Amend

C-DEBI Director

Do you have questions like:

• How do I put together (or understand) a budget?
• How do I improve my work-life balance?
• How can I use social media to help my science career?

If so, then this webinar series is for you!

Presenting the first of C-DEBI’s new professional development webinar series:

Leveraging Social Media

• Are you using social media to network and promote your science?
• Learn why you should and how to do it
• Led by Jen Biddle, Assistant Professor, College of Earth, Ocean, & Environment, University of Delaware
• Thursday, April 13, 12:00pm PST, connection link to follow

Our 2017 Networked Speaker Series speakers have been selected!  Please mark your calendars for this online seminar series to connect all of us interested “deeply” or broadly in the deep biosphere. Next month’s talk is by Dr. Annie Rowe at the University of Southern California, who will present “Eating rocks! Investigating microbial energy conservation with microbes that utilize solid mineral electron donors” on 3/9/17 at 9:30AM Hawaii Time/12:30PM PST/3:30PM EST.

Congratulations to the proponents of proposals selected for funding in our 2016 December call for research and education grants and fellowships. Stay tuned on our funded projects webpage for their exciting work in Phase 2 of C-DEBI!

• Graduate Fellowship: Lilja Strang (Advisor: Craig Moyer, Western Washington University)
  Insights into the genomics of deep subsurface vs. near surface Thermococcus isolates
• Postdoctoral Fellowship: Jeanine Ash (Advisor: Caroline Masiello, Rice University)
  Tracing deep biosphere methane cycling with clumped isotopes
• Postdoctoral Fellowship: Jesse Colangelo-Lillis (Advisor: Boswell Wing, University of Colorado Boulder)
  MEGA Analogue for Subsurface Sedimentary In-Vivo Evolution (MASSIVE) Plate
• Postdoctoral Fellowship: Abhiney Jain (Advisor: Jeff Gralnick, University of Minnesota)
  Taming a Zetaproteobacteria using genetics to understand iron cycling in the deep ocean biosphere: Mariprofundus ferrooxydans PV-1 as a model organism
• Postdoctoral Fellowship: Alma Parada (Advisor: Anne Dekas, Stanford University)
  Linking genetic diversity in benthic marine archaea to functional variability and contributions to carbon cycling
• Research Grant: John Dore and Eric Boyd, Montana State University
  Microbial anabolism in subseafloor sediments of the North Atlantic subtropical gyre: carbon vs. phosphorus limitation
• Research Grant: Dionysis Foustoukos and Costantino Vetriani, Carnegie Institution of Washington and Rutgers University
  Symbiotic Growth of Piezophilic Deep-sea Vent Bacteria
• Research Grant: Jessica Labonte and Peter van Hengstum, Texas A&M University Galveston
  Subseafloor prokaryotic and viral communities and interactions in anoxic marine basins: a case study from a 3000-year old stratigraphic succession
• Education Grant: Sharon Cooper, LDEO-Columbia University
  Stories from the Deep Biosphere: An Interactive Science Experience

Cheers,

Jan Amend
C-DEBI Director

CC-RISE is an eight-week, paid, summer research internship program for community college students run by the Center for Dark Energy Biosphere Investigations. Students will gain firsthand exposure to the scientific process by working in a faculty-led research lab at the University of California Santa Cruz or at the Woods Hole Oceanographic Institution in Woods Hole, MA. In addition to research, students will participate in activities focusing on how to transition from a two-year college to a university and information on graduate school. At the end of the program, students will present their results to an audience of peers and mentors. Applications are due March 20, 2017 for UCSC and March 24, 2017 for WHOI.

C-DEBI seeks nominations for three speakers for the 2016-2017 program. C-DEBI is continuing the NetworkedSpeakerSeries (begun in Fall 2011) as a means to enhance communication and the exchange of ideas among our spatially distributed community. Potential speakers can be nominated by colleagues, mentors, or those mentored by C-DEBI participants; they can also self nominate. Selected C-DEBI NetworkedSpeakers will make a presentation online, using video conferencing tools, with assistance from the C-DEBI main office at USC. Nominated C-DEBI NetworkedSpeakers should be capable of combining compelling visual materials with the ability to communicate effectively to a broad audience. We are particularly enthusiastic about giving young researchers a chance to present work to the C-DEBI community. Being selected to be a C-DEBI Networked Speaker is an honor. For more information about the SpeakerSeries and nomination request, please see: http://www.darkenergybiosphere.org/outputs-resources/networked–speaker–series/.

There are plans afoot to create a new federal 10-year ocean research plan (https://www.nsf.gov/geo/oce/orp/) to replace the plan created in 2007 and updated in 2013. This new plan will guide future federal funding, so it is vital that the science that we think is important is considered in the plan. To refresh your memory, C-DEBI scientists provided numerous comments on the 2013 update, and the impacts were undeniable in the resulting document. Now is the time to do that again! The public comment period on the draft societal themes and research goals is open until January 1, so there is not much time. It is only 7 pages, so take 10 minutes to read it.

We appreciate your commitment to C-DEBI and all its science, education, and outreach efforts. We are stronger together, evidenced again by the great interest in the latest call for research and education grants (13 graduate fellowship, 15 postdoc fellowship, 9 research, 3 education), which are currently being reviewed by C-DEBI Leadership and our E&O Steering Committee.

Happy holidays and best wishes for the new year!

Jan Amend
C-DEBI Director

C-DEBI’s NSF REU, C4, is a 9-week research internship targeting community college students nationwide. Students will spend their summer doing cutting edge research as they help grow, isolate, and describe previously unknown microorganisms. C4 students will work in teams in laboratories at USC, learning state-of-the-art techniques ranging from DNA sequencing to microscopy and sterile techniques to analytical chemistry. Applications due February 15, 2017.

The GEM Course is an all-expenses paid, three-week intensive introductory course in Global Environmental Microbiology (GEM) geared for early career undergraduates from 2 and 4 year institutions. The course focuses on microbes found in aquatic environments investigated through authentic research experiences (students collect, process & interpret data).  This residential course includes lectures, labs and fieldwork at USC and on Santa Catalina Island.

Where:  University of Southern California campus and Santa Catalina Island, CA
When:  June 11 – June 30, 2017
Who:  Undergraduates from 2 or 4-year colleges
Cost:  FREE, including travel, plus modest stipend
How to apply: http://www.darkenergybiosphere.org/education-diversity/for-undergraduates/gem-course/
Note:  First generation college, women, and under-represented students encouraged to apply

Application Opens:  December 05, 2016
Application Deadline:  February 01, 2017 at 5:00pm PST

For questions and comments, contact Gwen Noda at gnoda@usc.edu.

C-DEBI facilitates scientific coordination and collaborations by supporting student, postdoctoral, and faculty exchanges to build, educate and train the deep subseafloor biosphere community. We award small research exchange grants for Center participants. These grants may be used to support research, travel for presenting C-DEBI research at meetings, or travel exchanges to other partner institutions or institutions that have new tools and techniques that can be applied to C-DEBI research. We anticipate ~10 awards of $500-5000 with additional matched funds to be granted annually.

The NSF Science and Technology Center for Dark Energy Biosphere Investigations (C-DEBI) invites proposals for $15,000 on average (and up to $20,000) in direct funds for community workshops that will help to advance C-DEBI’s central research agenda: to investigate the subseafloor biosphere deep in marine sediment and oceanic crust, and to conduct multi-disciplinary studies to develop an integrated understanding of subseafloor microbial life at the molecular, cellular, and ecosystem scales. C-DEBI’s research agenda balances exploration-based discovery, hypothesis testing, data integration and synthesis, and systems-based modeling. C-DEBI welcomes proposals from applicants who would enhance diversity in C-DEBI and STEM fields.

Please join me in welcoming Gwen Noda as C-DEBI Diversity Director who in her few weeks at USC, has dived into leading our diversity efforts to serve our students, postdocs, faculty, and other participants at USC and across the nation. Ms. Noda is a Los Angeles native who earned her B.S. in Marine Biology and M.A. in Biology both from UCLA with a research focus on benthic aquatic invertebrates. She brings an extensive background in informal education in the field and classroom to support and grow our education and outreach programs, e.g., as former Co-Director of the Center for Ocean Sciences Education Excellence COSEE-West and coordinator of the FLOW Citizen Science Monitoring Program at Bolsa Chica Wetlands and State Beach for Amigos de Bolsa Chica among others.

We are also excited by a recent Nature Communications paper proposing a new bacterial phyla classification that highlights several C-DEBI persons of interest!  “Edwardsbacteria”, “Wallbacteria”, and “Nealsonbacteria” nod to our former Director Katrina Edwards, current External Advisory Board member Judy Wall, and colleague and grant recipient Ken Nealson. For details see the Banfield lab paper Thousands of microbial genomes shed light on interconnected biogeochemical processes in an aquifer system.

Cheers,

Jan Amend
C-DEBI Director

We have many things to celebrate! First, congratulations to USC graduate student Gus Ramirez for successfully defending his Ph.D. thesis; he now embarks on a C-DEBI Postdoctoral Fellowship with Steve D’Hondt at URI. Congratulations also to C-DEBI Senior Scientist Steve Finkel, who will receive the American Society for Microbiology’s 2017 William A. Hinton Research Training Award for outstanding contributions toward fostering the research training of underrepresented minorities in microbiology. Steve’s GGURE undergraduate research internship program is one of C-DEBI’s flagship STEM-retention programs.

We are also extraordinarily proud of C-DEBI Senior Scientist Victoria Orphan, recipient of a 2016 MacArthur Foundation Fellowship*. The 5-year “genius grant” is meant to encourage creative scientists, artists and other thinkers who are pushing the boundaries of their fields. Victoria is certainly doing that for C-DEBI. A true Californian, she spent her childhood in San Diego, received undergraduate and graduate degrees from UC Santa Barbara, did a stint at NASA Ames in Mountain View, and since 2004 has been on the faculty at Caltech—“Victoria, do you realize there are 49 other states and, according to the United Nations, 192 other countries?” She is a role model for all of us who do interdisciplinary science; she brilliantly combines field- and lab-based research with method development and state-of-the-art analytical approaches, inspiring junior scientists and the ‘more experienced’ among us along the way.

Cheers,

Jan Amend
C-DEBI Director

*Press: MacArthur Foundation, LA Times, New York Times, and Washington Post

C-DEBI invites proposals to support education and outreach projects, with a budget of up to $50,000 and a project duration of 1 year. The C-DEBI Education & Outreach Grants Program will fund the development of educational opportunities and materials that are pertinent to deep biosphere research in the subseafloor environment in support of our education and outreach goal to create distinctive, targeted education programs and promote increased public awareness about life below the seafloor. Help us further our mission to explore life beneath the seafloor and make transformative discoveries that advance science, benefit society, and inspire people of all ages and origins. C-DEBI welcomes proposals from applicants who would enhance diversity in C-DEBI and STEM fields. Proposal deadline: December 1, 2016.

C-DEBI invites proposals for 1-year research projects (in the anticipated range of $50,000-$80,000) and 1-2 year graduate student and postdoctoral fellowships that will significantly advance C-DEBI’s central research agenda: to investigate the subseafloor biosphere deep in marine sediment and oceanic crust, and to conduct multi-disciplinary studies to develop an integrated understanding of subseafloor microbial life at the molecular, cellular, and ecosystem scales. C-DEBI’s research agenda balances exploration-based discovery, hypothesis testing, data integration and synthesis, and systems-based modeling. C-DEBI research support is provided to “expeditions of opportunity”, and we’ve created a webpage listing potential options for participation. We welcome you to provide information about other expeditions of opportunity to share with the C-DEBI community! Help us further our mission to explore life beneath the seafloor and make transformative discoveries that advance science, benefit society, and inspire people of all ages and origins. C-DEBI welcomes proposals from applicants who would enhance diversity in C-DEBI and STEM fields. This request for proposals is open to all interested researchers at US institutions able to receive NSF funding as a subaward. Proposal deadline: December 1, 2016.

Greetings! Our annual call for research, fellowship, and education proposals is posted!  We continue to support research grants and graduate student and postdoctoral fellowships that will significantly advance C-DEBI’s central research agenda to investigate the subseafloor biosphere deep in marine sediment and oceanic crust, including on “expeditions of opportunity.” C-DEBI education & outreach grants will continue to fund the development of educational opportunities and materials that are pertinent to deep biosphere research in the subseafloor environment in support of our education and outreach goal to create distinctive, targeted education programs and promote increased public awareness about life below the seafloor. C-DEBI welcomes proposals from applicants who would enhance diversity in C-DEBI and STEM fields. Note, we have moved up the deadline for this call to December 1, 2016 to provide ample time for review by the anticipated notification date.

I look forward to continued, strong engagement by the community through our many C-DEBI programs and activities.

Cheers,

Jan Amend
C-DEBI Director