Research

Animal-Microbial Symbioses

Here at the Girguis Lab, we study how animals such as fish, clams, mussels, snails, and worms form symbiotic relationships with bacteria. Most of our work has been at deep sea vents and seeps, where many animals harbor intracellular “chemosynthetic” bacterial symbionts that harness energy from chemicals in vent fluid. They use this energy to convert inorganic carbon to sugars. They share these with their host, and as such are the primary source of nutrition for the animals. This partnership works so well that, in many cases, chemosynthetic vent communities can be more productive than rainforests and kelp beds.

The Girguis Lab is unique in that we study the ecological physiology of these invertebrates, utilizing shipboard experiments on live animals coupled to molecular analyses (e.g., qPCR, proteomics) to examine gene and protein expression in both the host animal and the bacterial symbionts. We build high-pressure systems that replicate in situ pressure and chemical conditions to understand how these animals interact with their environment. We also develop methods of sampling and fixing animals at the seafloor to analyze patterns of gene expression (e.g., the iSMASH blender). This will allow us to link our experimental work to analyses of the animals in their natural habitat. 

Extracellular Electron Transfer

Many microbes live in environments that are devoid of oxygen, i.e. anoxic habitats. Thus, unlike you and me, these microbes must devise a way to harness energy from “food” without using oxygen to drive that process. Anoxic habitats often do have other compounds that could substitute for oxygen ... if the microbes have the biochemical machinery to work with those compounds. 

Our lab studies a phylogenetically diverse subgroup of these microbes that can access oxygen substitutes and other molecules that exist outside their cells. They use a process called extracellular electron transfer (EET) to couple their internal metabolic pathways with external compounds such as minerals. We study a variety of mechanisms by which microbes may be capable of EET, such as direct contact with electrodes and/or minerals, electron transfer mediated by soluble redox shuttles, biogenic structures such as pili or other filaments, or biofilm formation. We seek to understand the role of EET in microbial energy metabolism in anaerobic environments. We are also interested in developing innovative technologies to harness microbial EET for sustainable energy production and biocatalytic processes.

Microbial Ecological Physiology

Broadly speaking, ecological physiology aims to characterize the nature and extent of how organisms’ physiological and biochemical capacities enable them to thrive in their environments, and ultimately shape their evolutionary fitness. The majority of our eco-physiological studies examine how deep-sea microbes flourish and interact in chemically-reducing habitats such as hydrothermal vents and hydrocarbon seeps. In particular, we aim to better understand the physiological mechanisms underlying key metabolic processes, e.g., methane and sulfur oxidation. We are interested in understanding the bioenergetics of these processes, and the implications for growth, reproduction, survival, abundance, and—to a degree—the geographical distribution of microbes. We are most focused on understanding the interactions among microbes that mediate these processes, and their influence on local and broader biogeochemical cycles. We examine these communities via in situ and ex situ experiments and develop new techniques and tools to address our questions of interest. Understanding the continuum of interactions among organisms and their physical and chemical environment requires expertise and appreciation of both ecological questions and biophysical, biochemical, and molecular methods and processes. Microbial ecological physiologists thus require a good understanding of both the molecular and cellular mechanisms underlying microbial metabolic processes, as well as the functioning of the microorganism in its environmental context.

Technology Development

To address our science questions, the Girguis Lab designs new technologies to study the molecular, physiological, biochemical, and metabolic processes among marine animals and microbes. Our technology development benefits from our formal training in marine sciences, as this allows us to develop tools that are well-suited to address the questions at hand. Our technologies include A) innovative high-pressure aquaria to keep deep-sea animals and microbes alive on board ship by re-creating the physical and chemical conditions found in the environment; B) underwater chemical sensors such as mass spectrometers, dissolved inorganic carbon analyzers, and stable carbon isotope analyzers; and C) a diversity of samplers that allow us to collect time-resolved fluid and microbial samples.

In the commercial marketplace, open source is a movement that promotes universal access to a product’s design or blueprint via a free license, to promote subsequent improvements by anyone, with the expectation that these too will be open source. A main principle and practice of open-source development is peer collaboration and bartering, with the end-product and documentation available at no cost to the public. This approach is quite common in software development and has been adopted to promote the development of “appropriate” technologies, and even drug discovery.

We believe that technologies developed with public funds should be made available as well, including associated designs and test data as appropriate. We strongly believe that an “open source” approach to disseminating technologies enables more rapid discovery and more efficient use of our community’s limited financial resources. When partnering with commercial entities, we make every effort to encourage “open source” approaches to development, and to ensure that any co-developed technologies are—at the very least—available to academic scientists at a reasonable price.