James Irvine Professor of Environmental Science and Geobiology
2010 - Present, Geobiology
I am interested in the mechanism of metabolic interaction between the two partner organisms in the AOM process. We recently found evidence supporting the hypothesis that electrons are directly shared between the two partners. I am investigating these ideas further by attempting to express and biochemically characterize the proteins that we think may be responsible. I am also interested in the better understanding the functional differences between ANME subgroups at higher phylogenetic resolution than has been previously been considered.
2015 - Present, Geobiology
My research involves anaerobic environmental microbiology in the context of laboratory-tractable systems. More specifically, I study spatial organization in syntrophies. In these systems, I am attempting to determine the patterns of spatial arrangement in partnered microorganisms and the role the mechanism of their interactions play to drive these patterns. Ultimately, I would like to use this data - derived from lab-grown cultures - and apply it to more intractable systems, such as those cooperative microbial interactions found in the environment. I also have a project studying division of labor in the context of the anaerobic chitin degradation pathway in seafloor mud.
2015 - Present, Geobiology
I'm interested in microbial metabolisms and the biogenesis of proteins that play important roles for biogeochemical processes in the environment. In the Orphan Lab, I'm developing a cell-free protein synthesis system to study enzymes that are central to archaeal methane metabolism. I'm also investigating the ecology and geobiology of microbial mats on Little Ambergris Cay.
Paul M. Magyar
2011 - Present, Geochemistry
My research is focused on better understanding nitrous oxide sources in the environment. I have developed new stable isotope mass spectrometry tools, which I am applying to the characterization of microbial nitrous oxide generation mechanisms. more
2014 - Present, Geobiology
I am interested in using analysis of microbe-mineral interactions in modern sediments and experiments to provide insight into unresolved problems in Earth history. Working in the Orphan Lab, I am focusing on disentangling complex interactions between microbial communities and their clay mineral hosts in seafloor sediments to understand how these communities can shape their mineralogical environment, which may provide clues to tracing the imprint of life on the rock record here on Earth and beyond. more
Sean W. Mullin
2013 - Present, Geobiology
My research interests are primarily focused around microbe-mineral interactions, especially as related to subsurface and deep biosphere communities. In particular, I focus on using micro-scale approaches to visualize the ways that microbes colonize various minerals as well as try to discern how the mineralogy affects the microbial assemblage in an area and the ways in which microbial metabolism can change the local mineralogy. We can do this using SEM, coupled Raman and deep-UV spectroscopy, as well as more familiar microbiological techniques like FISH microscopy and iTAG sequencing of 16S rRNA. I work with both in vitro and in situ communities, and the field sites I currently work in are a carbonate groundwater aquifer in Death Valley (~0.8 km deep) and the Subsurface Undgerground Research Facility in South Dakota (~1.5 km deep). I am also dabbling in making my own glasses with controlled compositions and redox states to use as a defined substrate for more precise experiments.
2016 - Present, Planetary Science
I am interested in the origins of life on rocky and icy worlds. How does the abiological (mineralogy, availability of water and pore space, availability of energy) inform the biological (microbial communities, metabolic staples) and vice versa? How do we study those connections in the rock record and modern extreme habitats?
Hang Yu (Hank)
2011 - Present, Environmental Science and Engineering
I am interested in the cycling of carbon and sulfur in deep sea methane seeps. This process is accomplished by a microbial consortia but their symbiotic mechanism remains elusive. Combining microcosms and meta-omics, my research aims to illuminate how this deep biogeochemical cycling is accomplished by the collaborative power of the small. more
2016 - Present, Biochemistry
I am interested in understanding the biochemical mechanisms that underlie microbial adaptation to unique environments. I use biochemical and biophysical assays to characterize proteins, particularly membrane proteins that are involved in novel electron transport chains. I am also interested in using fluorescence and electron microscopy techniques to look at samples with low microbial abundance.
2011 - Present
I work at the interface of geomicrobiology and organic geochemistry. I use techniques including microscopy, microbial culturing, lipid extraction and analysis, and stable isotope geochemistry with H, C, N and S to study microbial transformation of organic molecules and the molecular and isotopic imprints microbes leave behind in the geologic record. more
2013 - Present
The dominant predators of marine microbial communities – heterotrophic protists and viruses – are key structuring agents in ocean ecosystems. Given that marine microorganisms are major drivers of biogeochemical processes in the oceans, determining the distributions, rates and interactions of these predatory groups is critical for adequate representation of microorganisms in ecosystem models and for developing a predictive understanding of lower trophic level response to climate variability. The overall goal of my research is to characterize the composition, distribution, diversity, and interactions of microbial predators, with a focus on marine protists, over a variety of spatial and temporal scales to better understand their influence on community structure and ecosystem function. more
2016 - Present
My interdisciplinary research into the interactions between microorganisms and their abiotic substrates reflects my fascination with the biogeochemical interface. I grew up in Edmonton Alberta where cold (sub -40) winters precluded outdoor pursuits for a large part of year – instilling in me a love for the spring, sun, and ocean – I can never let a sunny day go by without poking around outside under rocks. I completed my PhD in Geology, Planetary Science at the Centre for Planetary Science and Exploration at Western University in London, Ontario Canada where I investigated the role impact cratering has on facilitating microbial colonization and the potential for microbial metabolism to be preserved as conspicuous geochemical patterns in the rock record. In the Orphan Lab I am part of the NASA Astrobiology Life Underground Team lead by Dr. Jan Amend at USC and a member of the SHERLOC team at JPL lead by Drs. Luther Beegle and Rohit Bhartia. In my role on all three teams I am involved in developing in situ flow through microbial colonization experiments at the Sandford Underground Research Facility to investigate microbial activity in the terrestrial subsurface by integrating microbial activity monitoring experiments with a pipeline at JPL to use deep UV Raman and fluorescence spectroscopy at integrated observational scales to identify and characterize microbial activity while retaining the spatial context of the colonization substrate. When I’m not in the lab I’m usually hiking, running, knitting, or playing the tuba.
2014 - Present
I am an early career microbiologist and bioinformatician currently investigating microbial communities from methanotrophic ocean sediments. I recieved my PhD in microbial ecology from the University of Queensland. My PhD research focused on metagenomic analysis of microbial and viral communities from engineered ecosystems found in wastewater treatment plants. Throughout my PhD I was at the interface of microbial ecology, chemical engineering, and computational biology and have gained many skills ranging from microscopy, reactor operation and computer programming. I love looking at genomes and developing hypotheses on ecology and physiology based on genomic data. My current role is predominantly in bioinformatics, however my background in molecular biology allows me to transition into wet-lab roles and to place the inferences of metagenomic data into a broader biological framework. more
2016 - Present
I'm interested in the physiology of microorganisms that (obligately) interact with other community members. My research focuses on the interactions within microbial communities using spatial organization at the micron scale. Most of my PhD work was focused on genome-resolved metagenomic analysis of microbial communities of varying complexity. Many of the genomes obtained using this method show indications of interaction with community members. As genome-resolved metagenomics is maturing, the majority of sequenced genomes will soon be derived from uncultured organisms. Both genome interpretation and testing of hypotheses generated from 'omics data are challenging with the existing model systems. Using microbial cooccurence patterns, I intend to enrich naturally occurring consortia to study the molecular basis for their interaction and to diversify the available model systems. more
2010 - Present
My research in the Orphan Lab focuses how microbes make a living at 2 cm and at 2 km below the seafloor. In the 2 cm regime, I study microbial partnerships at sea floor hydrocarbon seeps with techniques developed to isolate partnerships of interest for downstream genetic analysis (Magneto-FISH, online, PDF). Combining functional metabolic gene and identification gene analyses in successive Magneto-FISH isolation experiments highlights the middle ground of microbial ecology between the single cell and the bulk sample. In the 2 km regime, I study the metabolic potential for life in deeply buried coal and shale deposits with samples I collected on IODP Expedition 337. By incubating samples with a series of isotopically labeled substrates, both at Caltech and at our collaborators’ facility in JAMSTEC, we can search for actively metabolizing microbes with geochemical (catabolism) and nanoSIMS (anabolism) methods combined with genetic means of identification. more
2010 - Present
2006 - Present
My work in the lab focuses on characterizing the aerobic methane oxidizing bacteria that live in ocean waters and sediments, towards answering the question “what is the nature of biological methane oxidation in the ocean?” Any method you can imagine to try to characterize methanotrophic bacteria– I have probably tried! I’ve cultivated a few new lineages, and identified new biochemical pathways in these basal – trophic - level microbes. I’ve also used lots of culture – independent approaches, including developing new molecular tools to analyze these organisms specifically. I’ve quantified their abundances through defined geochemical zones and through that work also identified some very divergent players in the marine methane cycle. We’re just at the beginning of this story – stay tuned as we learn how much of the genetic potential for methane oxidation may transfer across phyla, how resilient the enzyme central to bacterial methane oxidation is, and what community shifts we expect to occur as the chemistry of the ocean continues to change.