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Exploring an Unseen World

All around us is an invisible world that, while most people don’t often think about it, has big effects on our own. As principal investigator (PI) of the Michigan Geomicrobiology Lab in the University of Michigan’s Department of Earth and Environmental Sciences, Gregory Dick and his staff get to explore that world each day, studying how microorganisms influence larger Earth processes.

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Sense of discovery and the ability to meld interests with work are the driving forces in this lab

“I’m just fascinated with the notion that tiny, unseen microorganisms can have a big effect on biological communities and on environmental and geological processes,” said Dick about why he got into microbiology. “I’m not exactly sure when I first put my finger on that, but I’ve been interested in that for a long time.”

He adds that when he first started doing research in microbiology as an undergrad 16 years ago, he was more interested in the role of microbes in disease but soon realized he was more interested in the microbes themselves than in the health and medical side of things. The aspect of life in extreme environments was also a big reason that Dick decided to pursue a career in microbiology.

“There’s a wide range of different conditions that life on this planet can thrive under, and that also extends to our concepts of life potentially beyond Earth, so that is a field called astrobiology that also drew me into this science,” he says.

Arti Tyagi at the biosafety cabinet.Because the world of microorganisms is so diverse, there’s a lot of variety in the research Dick’s lab does, with their main projects focusing on microorganisms in deep-sea hydrothermal vent systems, cyanobacterial mats, and cyanobacteria responsible for harmful algal blooms, which is a major water quality issue in the Great Lakes.

“We study how microorganisms grow and reproduce based on chemosynthetic energy that’s found at the deepsea vents,” Dick explains about the work his lab does deep in the ocean. “Another side of that is we’re interested in how microorganisms influence the chemistry of deepsea hydrothermal vent fluids and how those vents affect ocean chemistry.”

Dick adds that his lab’s research involving cyanobacterial mats gives the 1,400-square-foot lab a look into the past, since the mats “are living analogs of the types of microbial mats that covered Earth for large periods of its early history.”

Like those main research projects, the backgrounds of the lab’s 12 staff members are also varied.

“A lot of people are entering my lab with just their undergraduate degrees, and because my work is pretty interdisciplinary—we do microbiology but we also do oceanography and more environmental chemistry-type stuff—I take on students with various backgrounds, from biology to environmental science to even engineering,” Dick explains.

The Geomicrobiology Lab in the CC Little Building at the University of Michigan, Ann Arbor.Depending on the position, staff have anywhere from undergraduate degrees up to the PhD level in education. While staff fluctuates as students graduate, on average the lab has three PhD students, three postdoc students, three undergrads, and three regular staff members. The training that students and staff get when they start in the lab, most of which is taken care of by two full-time staff members, depends on their position and experience level.

“Some of the people in my lab do only computer work, so obviously the type of training they get is quite different than what someone who [does lab work] might get,” Dick says. “We don’t have a standardized training protocol or regimen—it’s based on the employees and what they’ll be working on, so it’s customized.”

Employees are kept busy with anywhere from a few dozen samples to a hundred each month—that number changes due to the variety of work in the lab, Dick says.

“We have a variety of different extents to which we characterize samples,” he explains. “In some cases we’re just quickly screening samples, and in other cases we might spend years on the same samples.”

A day in the life and staying organized

Many of the students, postdocs, and other lab members spend most of their days working on computers in the lab. Dick explains that because most microorganisms in nature don’t grow in culture, in order to study those organisms lab staff must extract DNA directly from natural samples—either from soils, lake water, or seawater. The lab then sequences DNA directly in those samples—a process called metagenomics that allows lab staff to understand those organisms through their DNA and RNA sequences without growing them in the lab.

“[Metagenomics] involves high-throughput, nextgeneration sequencing, really massive datasets that are complex and take a long time to analyze on the computer in terms of bioinformatics,” Dick says. “A lot of my lab members spend a decent amount of time on the computer connecting these bioinformatics analyses.”

However, that’s not the only way staff spend their time.

Chemical storage and balance area.“Other days, the whole day will consist of performing DNA extractions or extracting RNA and converting it to cDNA [complementary DNA],” Dick says. “Another day on the job may be spent out on a boat on the Great Lakes or on the ocean—so there’s a variety of different ways we spend our days here.”

With all that variability, weekly lab meetings are essential to keeping things organized and everyone updated on each other’s work. In addition, Dick also holds weekly one-on-one meetings with staff members in order to keep track of progress, and the lab uses a Google calendar for scheduling and to inform staff of when Dick is in the office.

Petri dishes for the cultivation of bacteria from the environment.As PI, Dick is in charge of mentoring the students and postdocs as well as giving them advice on their projects and the next phase of their careers.

“I see myself largely as a facilitator—facilitating communication, facilitating research, providing an environment where productive and cutting-edge research can take place,” he says. “I think peer mentoring is really important. I can’t solve every issue in the lab, but if we all put our heads together, we’re often much more efficient. I think that’s where communication really pays off.”

He adds that the mentoring aspect of his job is one of the things he enjoys most.

“I just recently had my first couple of PhD students finish, and that was very satisfying, to see students and to think about how much progress they’ve made through their PhDs,” Dick says, adding he also likes discovering new things. “I think that’s what gets a lot of us into science— the process of discovery, of uncovering new processes and new concepts. We also do a variety of fieldwork, including going on oceanographic expeditions or day trips on lakes to collect samples and conduct our science, so I really enjoy that as well.”

Finding out what his staff like to do best and helping them combine those passions with their work is the main way Dick motivates his staff. “My main strategy is to allow them to pursue their own interests, to be flexible,” he says. “I think that’s when staff are most productive—when they’re happy. Treating them well, with respect, and in a professional way [is also important].”

So much data

While there are many fun aspects to working in the Michigan Geomicrobiology Lab, the work isn’t without its challenges, a main one being the massive datasets lab staff have to work with on a regular basis.

Microscope room with Zeiss epifluorescence microscope.“That presents both conceptual challenges as well as just having computers that are big enough to crunch through some of this data to process it,” Dick says, adding that the extraordinary diversity and novelty of microbial life in nature are other things that can make the lab’s work difficult. “A lot of the organisms we study have never been brought into culture in the lab and are very, very different than anything that’s been brought into culture in a lab, so the biggest challenge is to infer their biology based on DNA- or RNA-sequenced information, especially when they’re very different from laboratory model organisms where we usually do our genetics and biochemistry and so on.”

To handle those challenges, the lab has a full-time bioinformatics specialist on staff to help Dick and the rest of the lab members keep up with all of the new technologies and programs in the bioinformatics field and to help train the rest of the staff in those newest approaches.

Dick adds that, without a doubt, the biggest change in the microbiology field over the past few years has been the improvement in DNA sequencing technologies.

“When I was a graduate student, DNA sequencing was much more expensive and we could generate much less data,” he says. “In the last ten years, the throughput has gone up and the cost has gone down, and this relates to some of the data challenges that we talked about earlier. It’s fundamentally changed the way that we do our science.”

As far as the lab’s future goes, lab members’ work with cyanobacteria is a new direction that will involve some construction.

“When I built my lab, we weren’t really set up to do that [cyanobacteria research], so a big part of my lab’s plans for the next few years is to build a photosynthetic cultivation facility where we can grow cyanobacteria,” Dick says.

Top 5 Instruments In The Lab

  1. Thermal cycler for polymerase chain reaction
  2. Biosafety cabinet
  3. Autoclave
  4. Zeiss epifluorescence microscope
  5. UV-VIS spec plate reader

In addition, the lab’s harmful algal bloom research, which they were just funded to do by the new University of Michigan Water Center, will get under way soon, as lab staff will be taking samples from Lake Erie each week this summer as part of the project.

“They [harmful algal blooms] really affect water quality and the quality of these lakes in terms of recreational value,” Dick says about the importance of the research. “We’re going to be applying some new genome and transcriptome techniques to these harmful algal blooms. To me, what’s cool about that is we’re studying interactions between bacteria and viruses and environmental chemistry and trying to understand how all that translates into this big societally relevant environmental issue.”