GrEBES Research.

Ashley Bateman: Ecology of skin-Associated microbial communities

2012-10-01 15.41.47I am a second-year graduate student in the Green & Bohannan Labs in the Institute of Ecology & Evolution. My current research uses principles of community ecology to help us study of the dynamics of the normal microbial communities that live on our skin. As a result of the Human Microbiome Project, we now know that human-associated microbial communities can vary in regards to the types and relative amounts of microbial species found. We also know that certain microbial communities can impact human health. The skin harbors a particular set of bacterial species (many of which overlap with other body sites), but with some dominant species that are unique to the skin. The skin is also the most variable of all of the body sites, meaning that the community changes over time and between individuals more than other body sites do (i.e. gut, oral, nose, & vaginal sites). Amazingly, these skin microbial communities are able to retain enough personalization that we can actually forensically identify items that a particular person has used, such as private computer keyboards. I am interested in understanding where our skin microbes come from and why skin microbial communities vary more than others.

I am particularly interested in defining how our interactions with the Built Environment influence the meta-community dynamics of our skin microbiome. We spend upwards of 70% of our time inside human-built habitats, yet we know astonishingly little about the microbes that share this habitat with us. I am a member of a collaboration of architects and scientists at the BioBE center that is trying to understand how the way we design and manage our buildings might influence the microbes that live inside them, and ultimately the microbes that live on ourselves. Contact Ashley.
Adam Burns:  Community ecology in the zebrafish gut.

As a member of the Bohannan lab, I study the assembly and dynamics of host-associated microbial communities using the zebrafish, Danio rerio, as a model system. The animal gut is host to a complex community of microorganisms, but despite the importance of these communities to host development and health, we still know very little about the forces that drive their assembly and structure. My research combines microbiological and molecular techniques with principles from community ecology to address this issue, with a particular focus on dispersal and applying metacommunity theory.

Metacommunities are collections of discrete ecological communities linked by dispersal. The zerbrafish intestine provides an excellent system for experimentally testing predictions from metacommunity theory. In addition to providing information about how microorganisms interact with their hosts, including humans, such research can also address questions about microbial communities in general, including: To what extent are microbial communities neutrally assembled? How does dispersal influence the diversity of organisms within a community (α-diversity) and between communities (β-diversity)? How does the ecology of hosts influence the ecology of the communities they are host to?  Contact Adam.

Alida Gerritsen: Genetic architecture of blood-feeding in mosquitos.

I am interested in the evolution of biting behavior in mosquitoes; part of my research involves identifying genes that are differentially regulated in response to the presence of a host. I am using many approaches, including RNAseq, RAD-tags, and ESEM imaging to further characterize the differences between biting mosquitoes and non-biting mosquitoes. And yes, non-biting mosquitoes do exist.

Potential undergraduate projects:

I am interested in different genes that are associated with host recognition. One project would involve identifying candidate genes from the genome and sequencing them in search of morphological differences, such as SNPs and indels. Another potential project would be to characterize the microbial gut flora of biting vs. nonbiting mosquitoes, starting from eggs all the way to adults. Both these projects would involve animal husbandry and molecular techniques such as DNA extraction, cloning, and sequencing.  Contact Alida.

Steve McAllister: Microbial ecology and biogeochemistry

I’m a PhD candidate in the Bohannan and Bridgham labs. I study the role of microbial community structure in controlling biogeochemical processes, specifically the production of methane in northern peatland ecosystems. These systems are particularly vulnerable to global climate change, and harbor vast quantities of soil carbon, making them the source of large fluxes of greenhouse gasses that have the potential to increase in the future.

The first half of my dissertation work focused on studying the varying rates of two different pathways of methane production in a variety of peatlands in northern Michigan, across multiple growing seasons. What substrates were most utilized for methane production? Did this change across time, or vary from place to place? How much of this variation can be explained by environmental variation, and how much remains unexplained?

Because different taxa of methanogens, the archaea responsible for methane production, utilize different substrates, I hypothesize that one important control on the relative rates of different methanogenic pathways is the structure of methanogen communities. I am now studying the community structure and activity of these organisms, by quantifying the presence and expression of mcrA, a key gene in methanogenesis in these sites. Do the abundances of various functional groups of methanogens co-vary in time and space with the dominate pathway of methanogenesis? Does transcription of mcrA vary with season? Do changes in transcription themselves vary by taxa? Can this information be combined with environmental data to produce a computer model capable of predicting methane flux from peatlands?

If you’re interested in the fusion of high-throughput DNA sequencing and data analysis with soil chemistry and global nutrient cycling, this may be the project for you! Work in the coming year will include analyzing a new sequence dataset, preparing mRNA libraries for sequencing, and measuring fatty acid content in archived peat samples to better understand the biogeochemical context of the bugs we’re studying! Contact Steve.

Thom Nelson: Adaptation and speciation in vertebrates


I am interested in adaptation to new environments and how the organization of the genome affects this process. Adaptation is complex, in part because it can involve interactions between many hundreds of genes. Because genes exist as regions of DNA on chromosomes, the physical structure of the chromosome affects how alleles of those genes are co-inherited from parent to offspring. I study how the arrangement of genes in the genome affects their co-inheritance and how that process influences adaptation. Specifically, I study chromosomal inversions in populations of threespine stickleback fish. Chromosomal inversions occur when a mutation event physically flips around a piece of a chromosome (so that a chromosome with genes ‘A-B-C-D-E-F-G‘ would become ‘A-B-E-D-C-F-G‘). The result is that this chromosome now has two forms – ‘standard’ and ‘inverted’ – and recombination between these two forms is severely reduced (region ‘C-D-E’ will not recombine with region ‘E-D-C’). If alleles of genes C, D, and E are adaptive to a specific environment, an inversion can essentially trap these alleles together.

I am interested in the causes and consequences of adaptive inversions. My research questions include:

  1. 1) How do adaptive inversions form and spread throughout a population?
  2. 2) What genes are involved, and how do these genes affect phenotype?
  3. 3) How do inversions contribute to reproductive isolation?

Contact Thom.

Lorien Reynolds: Soil-climate feedbacksDSC00147

I am fourth year student in the Bridgham lab.  My doctoral research is primarily focused on soil-climate feedbacks, specifically how the decomposition of soil organic matter (SOM) will respond to a warming climate.  My research has included monitoring indices of SOM decomposition as part of a larger warming-wetting experiment in upland prairies in the Pacific Northwest, as well as collaborating on a series of experiments exploring how SOM is incorporated into soils, how the rate of decomposition responds to temperature changes, and the implications these may have for future climate.  I utilize a number of field and laboratory methods to examine the carbon and nitrogen content of mineral soils, as well as indirect measures of microbial decomposition rates.  I am primarily interested in working at the interface between the biotic and abiotic, understanding how biogeochemical cycles mediate living systems from the ecosystem to the global scale. Contact Lorien.

Keaton Stagaman:  Ecology of host-associated bacterial communities.

I’m a 4th year PhD student in the Bohannan and Guillemin labs.  The primary goal of my research is to elucidate the ecological interactions between host-associated bacterial communities (microbiota) and vertebrate hosts.  In particular I am interested in understanding the role that the adaptive immune system plays in regulating the bacterial community, as well as how the bacterial community in turn affects the adaptive immune system, specifically the host’s antibody repertoire.  I use the zebrafish, Danio rerio, as a model organism to test specific hypotheses related to these general topics.  The questions I hope to answer are:

1.  How does the gut microbiota affect the development of the adaptive immune system?

2.  How does the initiation of adaptive immunity affect the diversity of the gut microbiota?

3.  How does manipulation of the gut microbiota affect the antibody repertoire?

4.  How does manipulation of the antibody repertoire affect the gut microbiota?

Contact Keaton.

Roo Vandegrift:  Plant-fungal interactions.

My research focuses on symbioses between plants and fungi. I’m specifically interested in the ways that playing host to multiple fungal symbionts affects the evolution of the host plant. I’m also interested in the role that fungal symbionts play in the dynamics of invasive plant species, and how fungal ecology is generally tied to plant or insect ecology.

To these ends, I have three major projects starting right now. The first is a field study examining competition between fungal symbionts in the roots and leaves of grasses across a climate gradient. The second is a greenhouse experiment testing the effects of a fungal symbiont on an invasive species of grass. And the third is a study of the ecology of a group of fungi associated with tree leaves in the Ecuadorian cloud forest.

All of these projects have a number of smaller offshoots that could form self-contained projects for the motivated undergraduate. The type of work I’m doing covers everything from field collections to DNA sequencing. Other work in the lab also focuses on fungal/plant interactions or invasive species ecology, so if you’re interest in these fields, this might be a good place for you.  Contact Roo.

Ann Womack:  Microbial ecology of the atmosphere.

I’m a fourth year PhD student in Jessica Green’s lab studying airborne microbial communities. The overarching aim of my research is to characterize the structure and function of microbial communities in the atmosphere. Microorganisms influence atmospheric processes through cloud formation and precipitation development and through the transformation of organic compounds, yet we know very little about the extent and variation of airborne microbial biodiversity and their role in the functioning of the atmosphere. The specific questions I am addressing with my research are: Is the atmosphere a habitat for metabolically active microbial communities? How does the structure of the metabolically active community differ from the total microbial community in the atmosphere? What are the sources of microorganisms in the atmosphere?  Contact Ann.


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