Progress 01/01/05 to 12/31/05
Outputs
Estrogens, which are widely used in agriculture and are resistant to wastewater treatment processes, cause the feminization of male aquatic organisms and cancer. The purpose of this study is to identify bacteria and genes responsible for estrogen metabolism in pristine and agricultural soils using culture-dependent and -independent techniques. An additional goal is to develop statistical software that microbial ecologists can use to characterize and compare microbial communities.
Impacts
This project will develop computational tools to characterize microbial diversity using rigorous statistical analyses while identifying novel 17B-estradiol degrading pathways and their host organism. By identifying these pathways, we will be better able to improve remediation strategies to maintain clean soils, lakes, streams, and drinking water. We successfully released three computational programs to the scientific community and had them published as four papers in premier environmental microbiology journals. We also developed an intracellular screening method that will make the screening of metagenomic libraries more efficient resulting in one publication. An additional two review articles have been published describing various elements of metagenomics.
Publications
- Schloss, PD & Handelsman, J. (2006). Introducing TreeClimber, a test to compare community structures. Submitted to Applied and Environmental Microbiology, In press.
- 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.
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Progress 08/15/03 to 08/14/05
Outputs
This project developed computational tools to characterize microbial diversity using rigorous statistical analyses. We successfully released four computational programs to the scientific community and had them published as four papers in premier environmental microbiology journals. We also developed an intracellular screening method that will make the screening of metagenomic libraries for estrogen remediating pathways more efficient resulting in one publication. Over the course of this project a total of eleven peer-reviewed journal articles were published.
Impacts
The statistical software developed through the funded research has already had a significant impact on the field of microbial ecology. These tools have been accessed by thousands of researchers and have been used in publications in journals such as Science, Nature, and PNAS. The funding also enabled the PI to secure a tenure-track position within the Department of Microbiology at the University of Massachusetts.
Publications
- 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.
- 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, In press.
- 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.
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Progress 01/01/04 to 12/31/04
Outputs
During the past year, I have developed tools that will enable us to detect microbial community composition changes upon exposure to estrogen contamination and have begun work on developing an intracellular screen to identify genes that are induced by the presence of estrogen. One tool S-LIBSHUFF evaluates whether two communities drawn from the same community using statistical analysis. Another tool assigns DNA sequences to operational taxonomic units (OTUs) based on the genetic distance between the sequences and then calculates various ecological parameters based on the relative abundance of the OTUs. I am continuing to develop other statistical tools that will be useful for comparing the microbial community structure in pristine and contaminated sites. I have been part of a team of investigators in the Handelsman lab developing an intracellular screen to identify genes from uncultured bacteria that produce products that induce quorum sensing systems. My hope is to
modify this screen so I can identify genes from uncultured bacteria that are induced by estrogen or degraded estrogen.
Impacts
This project will develop computational tools to characterize microbial diversity using rigorous statistical analyses while identifying novel 17B-estradiol degrading pathways and their host organism. By identifying these pathways, we will be better able to improve remediation strategies to maintain clean soils, lakes, streams, and drinking water.
Publications
- Schloss, PD & Handelsman, J (2004). The status of the microbial census. Microbiology and Molecular Biology Reviews. 68(4):686-691.
- 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.
- Riesenfeld, CS, Schloss, PD & Handelsman, J (2004). Metagenomics. Annual Reviews in Genetics. 38:525-52.
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Progress 01/01/03 to 12/31/03
Outputs
Since initiating the project, I have spent most of my effort developing techniques to describe soil microbial diversity using 16S rRNA gene sequences and the remaining portion trying to culture bacteria capable of degrading estrogen. I have been unsuccessful in isolating a bacterium that is capable of using estrogen as its sole carbon source. This may be due to a lack of such organisms in the soil I have selected (pristine Alaskan black spruce forest soil) or because they are not culturable. To address the latter possibility, I will employ the metagenomics approach described in the original proposal. Should this approach not work, I will identify an alternative soil that has estrogen degrading activity. I am finishing several projects that resulted in computer programs that microbiologists can use to add statistical rigor to their microbial ecology studies. These tools will enable me to characterize the microbial community that I am sampling from and determine how
well metagenomic libraries resemble 16S rRNA libraries. My colleagues and I submitted the results of the first project to the journal, Applied and Environmental Microbiology, titled, "Integration of microbial ecology and statistics: a test to compare gene libraries." We corrected and expanded an implementation of the Cramer-von Mises test statistic for making comparisons between single gene libraries. The net result of this implementation is an accurate, precise, rapid, and easy to use computer program, which we used to demonstrate that the previous implementation calculated erroneous p-values. We performed a meta-analysis that suggests with a high degree of confidence that 16S rRNA gene libraries constructed from soils collected in Madison, WI and Scotland contain different bacterial lineages. The second computational tool assigns gene sequences to operational taxonomic units (OTUs) based on the pairwise genetic distance between them and then calculates various ecological parameters
from the OTU frequency data. This analysis has enabled me to make several important points. First, previous attempts to assign sequences to OTUs using a distance-based criterion often introduced assignment errors and the process was laborious. Second, non-parametric richness estimators routinely underestimate the richness of a fully characterized community and are substantially lower than what has been reported using other analytical techniques. Finally, I was able to construct collectors curves for each bacterial phylum and for the bacterial domain in general using sequences deposited in the Ribosomal Database Project. Prior to the development of this software, such a large analysis would not have been possible. The analysis revealed that there is still a considerable amount of bacterial diversity to explore.
Impacts
This project will develop computational tools to characterize microbial diversity using rigorous statistical analyses while identifying novel 17B-estradiol degrading pathways and their host organism. By identifying these pathways, we will be better able to improve remediation strategies to maintain clean soils, lakes, streams, and drinking water.
Publications
- No publications reported this period
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