Previous Virtual Meetings

Changing the Field Culture (AKA What Happens on Field Should Not Stay on Field) [2.1 MB PDF]

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 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.

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.

• Martinez-Cola, Marisela. 2020. Collectors, Nightlights, and Allies, Oh My! White Mentors in the Academy. Understanding & Dismantling Privilege 10(1): 25-57.

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).

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.

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.

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.

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.

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.

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.

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.