2020 C-DEBI Virtual Annual Meeting Participants

Previous Virtual Meetings

2021 Virtual Meeting Series

Friday October 1, 2021 (10:30AM – 12:00PM Pacific Time)
Towards a More Holistic Understanding of Mentoring Best Practices

Marisela Martinez-Cola, Morehouse College

Collectors, Nightlights, & Allies, Oh My! : Advice for Strengthening Cross-racial Mentoring Relationships [2.4 MB PDF]

In this talk, Dr. Martinez-Cola identifies and describes three types of mentoring relationships she has encountered throughout her academic journey. Through a combination of storytelling and information sharing, Dr. Martinez-Cola hopes to inspire self-reflection that can lead to a deeper understanding of both mentors and protégés.

 

Friday September 3, 2021 (10:30AM – 12:00PM Pacific Time)
The Future of MBIO in IODP

 

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).

Presentations [9 MB PDF]

  • What is IODP?, Beth Orcutt
  • Recent Deep IODP Biosphere-Themed Research, Jessica Labonté
  • MBIO Facilities: Drilling Platform Types, Stephanie Carr and Beth Orcutt
  • IODP Technical Note 4: Recommendations for Microbiological Sampling… Aboard the JOIDES Resolution Following 20 Years of IODP Deep Biosphere Research, Jason Sylvan
  • Future of Scientific Ocean Drilling, Steven D’Hondt
  • Review of the Structure of IODP Panels, Committees, Decision Making, Applying to Sail or Request Samples, How People Get Involved, Jen Biddle and Jason Sylvan
  • Wrap Up, Beth Orcutt

 

Friday August 6, 2021 (10:30AM – 12:00PM Pacific Time)
Techniques for Isolating Persnickety Microbes

Roman Barco, University of Southern California

Lessons learned from studying marine chemolithoautotrophic communities on minerals

Iron-sulfides are some of the most abundant mineral types on Earth. In the deep-sea environment, iron-sulfides are commonly seen in sediments but also associated with hydrothermal vent fields, including seafloor massive sulfide deposits. An analysis of early microbial colonization on iron-sulfides was undertaken in the U.S. west and east coasts to gain perspectives on rapid utilization of iron-sulfides as potential electron donors by chemolithoautotrophic microbes with goals of understanding the interplay between neutrophilic autotrophic iron-oxidizing bacteria (FeOB) and sulfur-oxidizing bacteria (SOB). I will discuss the microbial ecology associated with these (and other) minerals and the opportunities that these setups provide for the successful cultivation of microaerobic FeOB and SOB, among other chemolithoautotrophs.

Ileana Pérez-Rodríguez, University of Pennsylvania

From microbes in nature to nature in microbes

Deliberate cultivation and isolation of microorganisms associated with rock-water reactions in oceanic crust provides direct understanding of microbial physiologies and metabolisms, and how they are expressed under controlled and measurable physicochemical conditions. Specifically, I will show how my cultivation studies with anaerobic hydrogenotrophs from seafloor and subseafloor environments inform understanding of microbial speciation and microbial community structure in hydrothermal ecosystems. Studying microbial responses to environmental parameters also advances their utility for biotechnological applications.

 

Friday July 9, 2021 (10:30AM – 12:00PM Pacific Time)
Techniques for Isolating DNA from Tough Samples

Jackie Goordial, University of Guelph

Squeezing DNA from a rock: DNA extractions from low biomass settings

In this tutorial I will draw on experience in mineral permafrost and ocean crust samples to discuss methods to obtain genomic material from low biomass samples. I will discuss how (and when) to tweak common commercial DNA kits for low biomass samples (including lysis considerations and elution alterations), the use of flow cytometry to concentrate cells, and finally – options for amplifying DNA for downstream analysis when you get very small amounts.

 

Friday June 4, 2021 (10:30AM – 12:00PM Pacific Time)
How to Build Capacity for a Thriving Research Lab at a PUI (Primarily Undergraduate Institution)

Rika Anderson, Carleton College

Conducting research with undergraduates at a small liberal arts college [10 MB PDF]

We will discuss how to build up a successful research program at a primarily undergraduate institution (PUI). We will cover topics like teaching and research expectations at small liberal arts colleges (SLACs) and other PUIs, how to strike a balance between research and teaching at PUIs, how to design projects that fit the undergraduate student timeline, how to recruit and retain students in a diverse and equitable lab environment, avenues of research funding, and publishing with undergraduate co-authors.

Terry McGlynn, California State University Dominguez Hills

How to develop an undergraduate research lab with long-term sustainability [1 MB PDF]

I will describe the great variety of PUIs, including the ranges of expectations and resources in small liberal arts colleges and regional public universities. I will discuss what what it’s like to operate an undergraduate-centered research program, and describe a variety of strategic approaches to maintaining an active undergraduate research laboratory over the duration of your career.

Additional resources identified by meeting participants:

  • Small Pond Science blog: About how scientists research, teach and mentor in all kinds of academic institutions, including teaching-centered universities with Terry McGlynn, Editor-In-Chief
  • The Chicago Guide To College Science Teaching: Terry McGlynn makes evidence-based teaching practices more accessible to scientists who aren’t prepared for a deep dive into educational jargon and theory
  • SERC: The Science Education Resource Center at Carleton College
  • Adding Research to a Class Facebook group: About building CUREs (course-based undergraduate research experiences)
  • NAGT and SERC’s Earth Educators’ Rendezvous: Learn about new teaching approaches, discover opportunities to get involved in research programs, prepare for an academic career, or discuss how to approach teaching and learning challenges in their classroom
  • PUIScienceSlack: Discuss teaching and research in the sciences at a primarily undergraduate institution
  • Project Jupyter online notebooks: Document research from students (or anyone) who are have left the lab group

 

Friday May 7, 2021 (10:30AM – 12:00PM Pacific Time)
New Microbial Physiology Techniques

Roland Hatzenpichler, Montana State University

Next-generation physiology: Why and how to measure microbial phenotypes under (close to) in situ conditions

We will discuss cutting-edge approaches to measure microbial phenotypes and metabolic activities under as close to in situ conditions as experimentally possible. We will focus on non-destructive techniques capable of observing individual bacterial and archaeal cells that can be followed up by additional methods to further characterize cells of interest. Specifically, we will discuss how substrate analog probing and stable isotope labeling techniques, in combination with fluorescence- or Raman microscopy-based observation of intact cells, can test hypotheses generated via metagenomics and lead us towards a deeper understanding of microbial ecophysiology. Maybe more excitingly, we will discuss how these techniques can be employed to turn traditional workflows upside down and design experiments in which the phenotype of a cell is examined first and the genotype second.

 

Monday April 5, 2021 (10:30AM – 12:00PM Pacific Time)
New Tools in Bioinformatics

Jake Weissman, University of Southern California

Estimating maximal microbial growth rates from cultures, metagenomes, and single cells via codon usage patterns

Maximal growth rate is a basic parameter of microbial lifestyle that varies over several orders of magnitude, with doubling times ranging from a matter of minutes to multiple days. Growth rates are typically measured using laboratory culture experiments. Yet, we lack sufficient understanding of the physiology of most microbes to design appropriate culture conditions for them, severely limiting our ability to assess the global diversity of microbial growth rates. Genomic estimators of maximal growth rate provide a practical solution to survey the distribution of microbial growth potential, regardless of cultivation status. We developed an improved maximal growth rate estimator (gRodon) and predicted maximal growth rates from over 200,000 genomes, metagenome-assembled genomes, and single-cell amplified genomes to survey growth potential across the range of prokaryotic diversity (the EGGO database); extensions allow estimates from 16S sequences alone as well as weighted community estimates from metagenomes.

Ben Tully, University of Southern California

EukMetaSanity: A customizable workflow for the gene prediction and annotation of Eukaryotic genomes

The prediction of protein-coding regions in eukaryotic genomes requires multiple computationally and time intensive processes to accurately determine gene structure. Generally, eukaryotic gene prediction relies on a combination of transcript evidence, protein homology, and/or sequence signatures. EukMetaSanity incorporates the steps, repeat prediction, ab initio gene prediction, and evidence-based gene prediction into a single pipeline that can determine high-quality intron/exon boundaries for novel eukaryotic genomes. Along with an implementation that takes advantage of the distributed structure of high-performance computing clusters, EukMetaSanity has the ability to annotate 100-1,000s of eukaryotic genomes/MAGs/SAGs in short time-scales relative to current implementations and approaches. And while the need for this level of parallelization is not commonplace, recent marine eukaryotic MAG datasets suggest that practical solutions at scale will be necessary soon.


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