Microbial Musings—Adam Arkin, Ph.D.—Senior Faculty Scientist, University of California, Berkeley
Dr. Adam Arkin’s research focuses on the synthetic biology of microorganisms, environmental genomics, and molecular ecosystems biology.
On today’s episode, you will learn:
- How many microbes exist in a single gram of soil, and how scientists conduct research in the lab to try to identify how all of these microbes interact and function as a community
- What bacteriocin is and how it can utilize a partial phage to kill other bacteria directly
- How to understand the longitudinal dynamic between viruses and bacteria
At the University of California, Berkeley, Adam Arkin, Ph.D. is researching one of his primary interests, which is how microbes (i.e. bacteria, archaea, viruses) transform the environment and impact various processes, including the processes that occur in our own bodies.
He is working on how to track and characterize groups of microbes, understand how they operate together, and determine the ways in which we may be able to intervene in order to get microbes to do things that are beneficial to us.
The largest projects he’s working on involve terrestrial environments, such as the subsurface of a watershed. In particular, Dr. Arkin and his team are researching the microbes in a field behind the Oak Ridge National Lab, where the soil is contaminated with uranium and has the highest level of nitrates on Earth.
In that location, microbes breathe in the metals and transform them to immobile and relatively harmless substances. Dr. Arkin explain how this may be applied to the agricultural arena in order to use microbes that mobilize nutrients for crops, protect them from pathogens, increase resilience to drought, and improve their ability to sequester carbon, thereby reducing greenhouse gasses.
He continues by discussing the potential of a human microbiome that is resistant to invasion by pathogens and allows us to make better use of nutrients. What’s stopping the development of this? Dr. Arkin explains that despite the growing amount of data being gathered in the field, there are still huge gaps in basic data about the composition and function of microbial genes in a wide range of conditions.
Consider, for example, that a single gram of soil contains one million microbes and about 10,000 different species of microbes, and that the human gut contains just as many, if not more. He explains the approach that has allowed his research and the research of others to show that most large community microbial dynamics can be described by much smaller numbers of pairwise interactions. In other words, predictions about a large community of microbes can be made based on observations of smaller number of pairwise interactions among community members.
In addition to all of this, Dr. Arkin takes a look at viruses and phages, bacteriocin, mechanisms of cell sensing, the various uses of phages (including those in the therapeutic realm), in what ways his research relies on machine learning and computational biology, and so much more.