Patrick SchlossAssistant Professor Phone: 413-545-6751 Ph.D.: Biological and Environmental Engineering, Cornell, 2002 |
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Research InterestsMicrobial Evolution and Ecology Our laboratory is housed in a newly refurbished space with ample laborotory and office space for researchers. We have a liquid handling workstation (i.e. robot), quantitive and conventional PCR thermalcyclers, pulse field gel electrophoresis, and other standard molecular and microbiology equipment. We are always seeking to recruit eager and exceptional potential graudate students to our lab. We are interested in understanding the factors that account for the temporal and spatial distribution of bacterial phylogenetic groups and functions. We find it intriguing that no two microbial communities from soil are alike. Perhaps more perplexing is the observation that although two animals are genetically and ecologically very similar, their gut communities are considerably different. Why? Characterizing the taxonomic and functional biodiversity of any microbial community is a daunting problem that requires robust experimental and statistical methods. To advance our research we have been involved in the development of culture-independent methods of describing the genomic and functional diversity within a microbial community and statistical software for describing and comparing microbial communities using data from culture-independent methods. We have begun to pursue this research using soil collected from Centralia, PA and in the guts of Drosophila melanogaster.
Community formation in soil In the early 1960's the people of Centralia, PA realized that the coal vein that was beneath their small town had caught on fire from the burning of trash in a nearby landfill. This coal fire has been burning for the past 40 years and will continue to burn for several hundred more years. What is striking is that despite the intense heat generated by the fire, the area surrounding the affected soil is populated with grass, bushes, and trees. This indicates the presence of microbial communities that service plant life. In fact, we have been able to isolate bacterial DNA from soils above 80ºC. As the fire moves through the site cracks are formed in the soil that allow hot gasses to vent to the surface and effectively sterilize the surrounding soils. With time, the cracks collapse and the temperatures cool. Plant life will return when the soil temperatures decline to ~60ºC. Although there is a clear successional process for plant life, succession of microbial communities must precede the succession of plants. Using the soils affected by the Centralia coal fire, we are addressing the fundamental ecological problem of succession and whether there are assembly rules for microbial communities in soil. Ecologists have divided succession into two types - primary and secondary. Primary succession focuses on the development of a community that is not influenced by a previous community and secondary succession focuses on the development of a community where elements of the previous community still remain. We are carrying out a natural experiment to study primary succession of soil microbial communities in soils that are above an underground coalmine fire in Centralia, PA. Soil microbial communities are among the most diverse in the biosphere. A single gram of soil is generally composed of 109 cells distributed among thousands of different species. Added to this complexity is the common observation that no two soils are alike in their taxonomic membership and structure. These observations give rise to an important question: how do such high levels of microbial diversity arise? Are the bacterial populations specialists for particular temperatures or generalists? These questions address the mechanisms of succession and whether these mechanisms are deterministic (i.e. niche-differentiated) or stochastic (i.e. neutral). To address these questions we are employing a number of experimental and statistical approaches. Our lab is currently analyzing the taxonomic biodiversity of the site using 16S rRNA gene sequence collections obtained using convential PCR and cloning methods as well as cloning-independent pyrosequencing methods. To analyze the functional biodiversity of the site, we have begun to construct and analyze large-insert metagenomic libraries (~40 kb per insert) for genes that encode hydrolytic enzymes. These methods will enable us to understand the factors that account for the distribution of bacteria in the environment. Community formation and adaptation in the gut of Drosophila melanogater Before birth, each us of us was sterile. Once born, an intricate cascade of events results in the colonization of our stomach, intestines, and skin. Each of us is comprised of 1012 genetically identical human cells and 1015 diverse microbial cells representing hundreds of species. Each of these microbial species is part of our symbiotic microbial community that supports our digestion, vitamin production, and immune system. A natural question is, "Where does this community come from?" One hypothesis is that microorganisms are vertically transmitted from mother to child - this is certainly the case with Aphids and their Buchnera aphidicola endosymbionts. A second hypothesis is that the microorganisms are horizontally transmitted through the environment - this is the case with the bobtail squid, Euprymna scolopes , and the colonization of its light organ by the bacterium Vibrio fischeri. But what about other, less specialized, relationships? Much research has shown that the gut communities of animals born to the same mother are more similar to each other than to animals born to another mother; however, there is considerable variation in the degree of simlarity between individual born to the same mother. We hypothesize that while most of our initial community is donated by our family, environmental and developmental factors have an equally signicant impact on the structure and function of the gut microbial community.To evaluate this hypothesis, our laboratory has begun to use insect gut communities as a model system for understanding the relationship between hosts and their symbiotic communities. The first approach we are pursuing uses Drosophila melanogaster as a model system to explore the coevolution of the gut community with its host. Drosophila melanogaster and bacteria have independently been used to study evolution. Yet there is a paucity of examples studying the evolution of members within a community or between a host and its symbiotic community. We will use Drosophila melanogaster in experimental evolution studies with an emphasis on understanding how the gut community is changing. The second approach is a natural experiment approach. We will be attempting to correlate the population genetics of the insect host with the community composition of its gut community. By pursuing lab-based and natural experiments we will be able to transfer the knowledge we gain in the laboratory to natural systems and vice versa. We are employing a series of culture-independent and -dependent techniques to address these problems. Using culture-depenent techniques we can explore the intra-insect population genetics of the dominant organisms with the goal of linking that to insect population genetics. Further, useing culture-independent techniques such as 16S rRNA gene sequencing and metagenomics we can better understand the inter insect variation by obtaining a more complete picture of the taxonomic and functional biodiversity of the insect gut. Representative publications of our work include...Delalibera, I Jr, Vasanthakumar, A, Burwitz, BJ, Schloss, PD , Klepzig, KD, Handelsman, J, & Raffa, KF. (2007). Composition of the bacterial community in the gut of the pine engraver, Ips pini (Say)(Coleoptera) colonizing Red Pine. Symbiosis. 43(2):97-104. Schloss, PD & Handelsman, J. (2007). The last word. Annual Reviews in Microbiology. 61:23-34. Vasanthakumar, A, Delalibera, I Jr, Schloss, PD , Handelsman, J, Klepzig, KD, & Raffa, KF. (2006) Characterization of gut-associated bacteria in larvae and adults of the Southern pine beetle, Dendroctonus frontalis Zimmermann. Environmental Entomology. 35(6):1710-1717. Curtis, TP, Head, IM, Lunn, M, Woodcock, S, Schloss, PD , Sloan, WT. (2006). What is the extent of prokaryotic diversity? Philosophical Transactions of the Royal Society B: Biological Sciences. 361(1475):2023-2037. Schloss, PD & Handelsman, J. (2006) Introducing SONS, a tool for OTU-based comparisons of membership and structure between microbial communities. Applied and Environmental Microbiology. 72(10):6773-6779. Schloss, PD & Handelsman, J. (2006). Toward a census of bacteria in soil. PLoS Computational Biology . 2(7):e92. Schloss, PD , Delalibera, I. Jr., Handelsman, J, & Raffa, KF. (2006). Bacteria associated with the guts of invasive and native wood-boring beetles. Environmental Entomology . 35(3):625-629. Schloss, PD & Handelsman, J. (2006). Introducing TreeClimber, a test to compare community structures. Applied and Environmental Microbiology. 72(4): 2379-2384. Williamson, LL, Borlee, BR, Schloss, PD , Guan, C & Handelsman, J (2005). Genes for quorum sensing in uncultured bacteria from Alaskan soil. Applied and Environmental Microbiology. 71(10):6355-6344. Schloss, PD & Handelsman J. (2005). Metagenomics for studying unculturable microorganisms: cutting the Gordian knot. Genome Biology. 6(8):229-233. Schloss, PD & Handelsman, J. (2005). Introducing DOTUR, a computer program for defining operational taxonomic units and estimating species richness. Applied and Environmental Microbiology. 71(3):1501-1506. Schloss, PD & Handelsman, J (2004). The status of the microbial census. Microbiology and Molecular Biology Reviews. 68(4):686-691. Riesenfeld, CS, Schloss, PD & Handelsman, J (2004). Metagenomics. Annual Reviews in Genetics. 38:525-52. Schloss, PD, Larget, BR, & Handelsman J. (2004). Integration of microbial ecology and statistics: a test to compare gene libraries. Applied and Environmental Microbiology. 70(9):5485-5492. Schloss, PD & Handelsman, J (2003). Biotechnological prospects from metagenomics. Current Opinions in Biotechnology. 14(3):303-310. |
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Mailing AddressPatrick Schloss |
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