Current Research

From Bacteria and Archaea to plants to eukaryotes, researchers in CLEE use state of the art techniques to understand how life persists in some of the most extreme habitats on Earth. Scroll down to learn more about the many research groups working in CLEE.

Extreme Archaea and Bacteria

Bartlett, Iwata-Reuyl, Nadeau, Napier, Reysenbach, Perona, Thompson

Once thought to be grouped together with Bacteria, microorganisms in the domain Archaea possess characteristics of both bacteria and eukaryotes in ways once considered impossible. The Bartlett lab focuses on transcription, the first step in gene expression, in microbes from the domain Archaea.  While structurally similar to bacteria (their DNA is not enclosed in a cell nucleus), archaeal transcription machinery better resembles that of eukaryotes (organisms with cell nuclei). This, along with their relatively simple genome, makes them an ideal model for studying transcription.

Using a species of archaeon found in hot springs (Pyrococcus furiosus) as a model organism, the Bartlett Lab explores transcription using multiple approaches (working with live cells, isolated compounds, and bioinformatics). Their goal is to better understand transcription in archaea, and perhaps find out what archaea can tell us about transcription in all organisms, including humans.

Since the techniques the lab use involve precise manipulation of proteins and genetic material, they also have use in customized solutions to problems in chemical or biological engineering. One example would be applying tools from the study of P. furiosus to create variants on its heat-tolerant proteins for use in high-temperature industrial processes. In addition, since transcription occurs in all life, the Bartlett Lab’s work contributes to a body of knowledge that is applicable to life science. The true long-term impact of this work may not be in its direct applications, but its role in the broader conversation about life.

 

Proteins are among the most abundant molecules in living systems and have a diverse array of functions. The Iwata-Reuyl lab researches the chemistry that underlies biology, through the structure and modification of such proteins. Primarily, this research focuses on studying protein evolution and the chemical reactions proteins create to generate new functionality.

Many of the protein systems examined by the Iwata-Reuyl Lab are present in hyperthermophiles –understanding how these systems enable organisms to live at high temperatures is an important aspect of the research. Additionally, the lab studies the modification of nucleosides, a compound found in RNA, as well as DNA and proteins. Nucleosides are modified through ‘post-transcriptional processing’ (a process where primary RNA is converted to mature RNA) in bacteria. The lab focuses on bacteria and archaea, which has led to the identification of a number of bacterial organisms throughout the study.

Some bacterial systems currently worked with by the lab are pathogenic, allowing the researchers to work to develop and explore these systems as possible sites to target with new antibiotics. One system in particular is present within the human body, and when nucleosides are missing from the system, the cells become associated with fast dividing cancer. It is possible that the system is involved in keeping cells in check so that they do not enter a precancerous or cancerous state, therefore the Iwata-Reuyl Lab’s research could influence cancer research in a larger scale.

 

One of the greatest challenges in searching for life in extreme conditions is to build technology that survives to record and transmit images. Research in the Nadeau Lab aims to design new technology to detect and identify microbial life in extreme planetary environments. Within the past three years, the Nadeau Lab developed the first working prototype of a microscope for Digital Holographic Microscopy (DHM). The goal is to look for life in high ionizing radiation environments that are impossible for any currently available microscope to work under. The data budget for sending pictures is very low, so data that is sent back must be chosen carefully and be of high quality. These variables make detection of life on other planets a much bigger challenge than detecting life on Earth.

The research utilizes the best analog sites on earth to look for life, but when looking for life 10 au away, with a cover of radiation and temperature of 150 degrees Kelvin, it can be a challenge. The importance of finding life on another planet, even if that life is on the scale of bacteria is extreme.

Another possible impact of this work is through quantitative face imaging that can show researchers cells as they deteriorate in health. Many are interested in this type of microscopy for the diagnosis of cancer and biopsy specimens. Eventually patients may be able to swallow a microscope to aid in diagnosis. For example, the Heliobacter pylori bacteria involved in an ulcer infection are microscopic, so a patient could swallow a microscope and use image data to determine a diagnosis. This technology could help in catching diseases much earlier, but the size needed for ingestion is not yet available.

 

Sepsis is a detrimental immune response to infection that leads to life-threatening organ failure in humans and is the tenth leading killer in the world and the first killer of patients in the ICU. The Napier Lab studies the immune response to sepsis and works to identify and manipulate specific factors that initiate and drive sepsis severity in infected patients. Research in the lab focuses improving mechanisms to identify populations of people that are more susceptible to sepsis, and to develop new therapeutics to help treat septic patients.

Sepsis has existed for as long as medical records have been kept, dating as early as ancient Egyptian times. The lab is interested in identifying the differences that exist between septic patients and non-septic patients who have identical infections. A non-septic patient can eventually recover from a standard infection with antibiotics, whereas a septic patient’s blood vessels collapse, causing organ failure. What are the factors that cause this disease, and why?

Studying the effects of obesity and diet can also help us understand how different diets can manipulate immune responses to sepsis. By examining septic mice fed a standard diet versus septic mice that are fed an obese diet (also known as the Western Diet); we have been able to identify patterns in infection, which may eventually help medical professionals treat this disease.

 

Much life on Earth is not limited to the same narrow temperature range as humans are. In fact, many bacteria and other microorganisms, known as thermophiles, thrive in a scalding environment. Research in the Reysenbach lab focuses on the discovery and study of these heat-loving bacteria living in hot springs of all types by converting available geochemicals into energy (e.g., Aquificales, Aciduliprofundum boonei). Even after decades of research, so much about these microbes is yet unknown to the scientific community—their amazing metabolisms, their range in biodiversity, the nature of their unique settings—not to mention that new thermophiles are still waiting to be discovered.

The Reysenbach Lab collects samples from hot springs around the world, from Yellowstone National Park to thousands of meters below sea level along the edges of ocean-covered volcanoes. These samples allow Reysenbach and her colleagues to characterize and study how these unique geological and geochemically rich environments shape life for their native microbe communities. They can also search for answers as to what links this foundational microscopic life has to the macroscopic scales it supports.

These samples travel back to PSU where the Reysenbach Lab recreates conditions around the vents in order to observe the organisms. The lab analyze their genes, study how they transform their environment, and discover whether they have unusual properties that could provide medical, bionano-technological, and other industrial or humanitarian benefits. Ultimately, these microbes could also help offer hints at how life might have evolved on this planet and inform exploration for signs of past life elsewhere in the solar system.

 

Many questions surround the origins of life, due in large part to the inhospitable nature of the anoxic early Earth. The Perona lab seeks to answer some of these questions, using techniques including genetics, biochemistry, bioinformatics, and x-ray crystallography. The lab studies methanogens – archaea, and bacteria that use reduced compounds such as sulfur, instead of light, to make energy who were present during the transition from a non-aerobic to aerobic Earth. By analyzing the molecular structure of methanogens, the lab has discovered new genes that may be used micro-organisms thriving in present-day extreme environments, such as the deep sea.

 

Understanding how life survived on early Earth also provides insight into the future, and studying methanogens supplies important critical knowledge in how the earth’s carbon cycle affects a changing world. For example, the Perona Lab is currently investigating how organisms could use carbon dioxide in the atmosphere instead of light, to create artificial photosynthesis and synthesize oxygen, and to help mitigate increasing atmospheric carbon emissions. The Perona Lab utilizes combined expertise in law and biochemical study of methanogens to influence governmental policymaking in the areas of climate change, renewable energy, and biotechnology. This work also adds to the pool of knowledge that other scientists interested in biochemical and elemental cycles can pull from and build upon, by helping us to understand the origins of life.

 

 

The microbe Prochlorococcus (Pro for short) is the most abundant photosynthetic cell on Earth, inhabiting upper depths throughout the world’s open oceans. Research in the Thompson lab focuses on Prochlorococcus, one of the building blocks of Earth, to gain a better understanding of the role of marine microorganisms that make up the world, as we know it. To understand our everyday experience on Earth, we have to study the building blocks that make up the system as a whole. While most people may think that the oxygen we breathe is from plants and trees on land, it is actually generated by the tiny marine phytoplankton inhabiting our world’s oceans.

Most of the oceanographic samples come from Station ALOHA, located in the middle of the Pacific Ocean, taking almost a full day to get to by boat from Hawai’i. Dr. Thompson takes samples from different depths to measure temperature and nutrients in the water, as well as observe the changes in Pro during different weather events or seasons.   

 

Extreme Eukaryotes

Buckley, Podrabsky

Many species of fish can survive only narrow range of temperatures, and for some, this means flourishing at freezing temperatures. The Buckley lab investigates physiological responses of marine species to elevated temperatures and other stressors. The lab studies fish from a variety of habitats – one primary area of focus is on the Antarctic notothenoid fish, inhabitants of one of Earth’s coldest environments, possessing a unique biology that holds unexplored scientific secrets. The Buckley Lab works to understand the unusual biological processes these fish use for survival to shed light on the impacts of climate change on marine species and possibly even to help find the cure to certain cancers.

“Off-model species” are unusual species with unmapped genomes. Using genomics-enabled technologies the Buckley Lab works to characterize broad-scale patterns of environmentally controlled gene expression, with the goal of linking these patterns to phenotypic changes at the cellular and organismal level. In adapting to sub-zero waters, Antarctic fish, such as the emerald notothenoid (Trematomus bernacchii), utilize biological processes unique among aquatic life. The research shows how the proteins at work in emerald notothenoids can influence human medicine. He also tracks how even small changes in the climate can have huge impacts on these fish and their surrounding ecosystem.

The Buckley Lab has already uncovered several potential applications for this research. A protein within the emerald notothenoids (C/EBP-δ) has been shown to inhibit certain cell growths when activated by temperature changes. Research suggests that this protein, combined with heat treatments, could shut off the growth of some human cancers without the need for chemotherapy. The same research provides actionable data showing how climate change will affect these fish and the surrounding ecosystems.

 

While most fish require constant submersion in well-oxygenated water to survive, small cyprinodont fish inhabiting the deserts of southwestern North and northern South America thrive in ephemeral desert pools. The Podrabsky lab studies the how the Annual Killifish (Austrofundulus limnaeus) is able to arrest its embryonic development during the dry seasons of South America. Living in an environment subjected to periodic drought, these fish tolerate extremes in temperature, oxygen, pH, and salinity. Additionally, the embryo stays dormant, without oxygen, in dried up pond mud for three months. When the rains come again, the ponds reform and eggs quickly develop into adulthood with the reintroduction of oxygen.

Dr. Podrabsky and his team have published the first-draft genome for the Killifish species. Additionally, the lab has recently discovered that the molecular pathway related to dormancy is linked to Vitamin D signaling and the regulation of the hormone calcitriol. Understanding how an organism develops in its natural environment at the embryonic level is critical to understanding how organisms evolve, adapt through time, and respond to climate change. Studying the arrest in cell proliferation during the development stage also has implications for cancer therapy. The study of anoxia (the absence of oxygen) and hypoxia (the absence of enough oxygen in the blood to sustain bodily function) in killifish could lead to a better understanding of treatment or therapy for human heart attacks and stroke.
 

Extreme Plants and Bryophytes

Ballhorn, Eppley, Rosenstiel

Plants cannot escape when attacked by herbivores and pathogens, or when exposed to unfavorable conditions, but they can defend themselves through a combination of defensive traits and ecological interactions. The Ballhorn Lab works to understand the indirect and direct defenses of plants against herbivores and pathogens, including plant biochemical defenses and microbial (bacteria and fungi) interactions.

Like humans, plants have ‘friendly’ ecosystems that live and thrive within them; complete with not only bacteria, but also fungi and more. Current research focuses on two avenues of plant defense: understanding 1) the molecular and ecological interplay of biochemical plant traits and 2) the role microbes play in helping plants to better face the changing and increasingly extreme environments they reside in. With a parallel approach of culture-based isolation and next-generation sequencing, the Ballhorn Lab utilizes gas chromatography and chemical analysis to gain a better understanding of the impact of micro communities on plant chemical phenotype and their mediation of stress tolerance and defense.

A major focus of the Ballhorn Lab is to begin to understand how to build plant systems better able to face the changing conditions of the world. In this research, among other benefits, lies the potential for the creation of Symbiotically Modified Organisms (SMO) to modify the microbiome and shift plant traits in ideal directions.
 

Plants combat various challenges during sexual reproduction, many of which mammals and other animals do not encounter. For plants, the environment itself can be the source of the strongest difficulties. The Eppley lab studies how stresses on plants in extreme environments affect their sexual reproduction, in particular that of certain bryophytes (mosses) and angiosperms (grasses, in particular). Although most plants can reproduce asexually as well, sexual reproduction has advantages for maintaining genetic diversity.

For over 20 years, Dr. Eppley has studied the effects of sea-level rise on the salt marshes on the Oregon and Washington Coasts. As sea-levels rise, salt marshes, which are an essential interface between the terrestrial and the marine coastal ecosystems, move up to higher ground. The Eppley Lab studies a species of salt marsh grass (Distichlis spicata) with separate female and male plants. The lab is interested in how the grass’ mutualistic relationship with microbes in the soil will change with the rise of salt levels and how this will affect sexual reproduction in the grass.

In Antarctica, Dr. Eppley studies how glacial retreat affects sexual reproduction in mosses. As Antarctica warms, the conditions for mosses change, actually improving the environment for sexual reproduction. Male mosses do not thrive in extremely cold temperatures, so the warming trend increases the number of male mosses in the ecosystem. The warming of Antarctica is the first time the scientists have been able to study the terrestrialization, or the retreat of the glacial ice, of an entire continent. The lab’s research contributes to knowledge about how complex ecosystems change over time in order to improve predictions about how global climate change will affect them.

 

Bryophytes (mosses and lichens) are quickly taking over surfaces exposed by retreating Antarctic glaciers and the biophysics of this process are increasing surface temperatures. Research in the Rosenstiel Lab is focused on how the growing presence of these extremophiles shapes ecological processes and influences both local climate and biology of the atmosphere.

Working in Antarctica, Rosenstiel and colleagues seek to understand how surface warming affects the biology of terrestrial bryophytes and their associated ecological community. Reproductive spore growth from the fungi and bacteria on the bryophytes suggests that warmer conditions are favorable to increased growth. These spores (produced in the tens to hundreds of thousands) are suspected of creating more rain regionally and providing accelerated feedback, which is crucial to account for, but often missed in climate change models. The scientists also measure emissions of volatile organic compounds (VOCs) into the Antarctic environment, which are also likely produced by mosses and lichens. By studying not only bryophyte growth but also their impact on geochemistry and the biology of the atmosphere (lower troposphere), the Rosenstiel Lab aims to connect many pieces of the ever-complex climate change puzzle.

In exploring how these bryophytes are colonizing the continent of Antarctica, the research provides data for understanding their potential uses in stabilizing other planets. Having survived four mass extinction events due to their great diversity, bryophytes can survive in the most extreme of environments and are an excellent group of organisms to consider for possible answers in climate change stabilization.

Extreme Viruses

Stedman

Viruses can be found everywhere on Earth, and their ability to survive in a range of conditions make them ideal candidates for study in evolution and diversity. The Stedman lab utilizes a suite of genetic, comparative genomic, structural and biochemical approaches to study viruses found in high-temperature, acidic environments such as volcanic hot springs.  Some of these viruses are unique, making them ideal subjects to study how viruses evolve, adapt, and survive under extreme conditions. Understanding how viruses behave and evolve advances scientific knowledge that can have use in to combating diseases like cancer as well as providing vital clues about how life began on Earth.

One area of focus in the Stedman Lab is on the extremely thermophilic viruses from the genus Sulfolobus (Archaebacteria), which are different from any other viruses in both their structure and genetic material. Thermophilic organisms live in high-temperature habitats—between 106° and 176° Fahrenheit and these new Sulfolobus in a hot, acidic lake. Research in the lab has discovered that these viruses appear to have been formed by an unprecedented RNA-DNA recombination event. The Stedman Lab is working with other [non-infectious] “cruci” viruses in the lab, trying to recreate a cruci-virus recombination like the one they found in the acidic lake.

A second area of research in the Stedman Lab is virus silicification, the first step in the formation of virus fossils. This process involves coating a virus in silica to inactivate it reversibly, which has significant implications for developing more shelf-stable vaccines. Silicification efforts led Dr. Stedman to found a new company called Stones Table, Inc., which is working to perfect this process; it has the potential to revolutionize vaccine formulation and save millions of lives.