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Your search keyword '"Hazen, T. C."' showing total 140 results
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140 results on '"Hazen, T. C."'

2. Development and applications of GeoChip 3.0 for analysis of microbial community structures, compositions, and potential functions

Author

He, Z., Deng, Y., Nostrand, J. D. Van, Wu, L., Hemme, C. L., Gentry, T. J., Liebich, J., Tu, Q., Arkin, A. P., Hazen, T. C., and Zhou, J.

Subjects
microarray, functional gene, microbial community
Abstract

: Functional gene arrays (FGAs), or GeoChip constructed with key genes involved in various biological and geochemical processes have been widely used to analyze microbial communities. Based on GeoChip 2.0, a new generation of GeoChip (GeoChip 3.0) has been developed. GeoChip 3.0 has several new features in terms of coverage, design, and data analysis. GeoChip 3.0 covers approximately 50,000 gene sequences for 306 gene families, and especially functional genes involved in antibiotic resistance and energy metabolism, and phylogenic marker GyrB have been added, which allows us to obtain more information about microbial communities and analyze more diverse environmental samples. For probe design, sequence-specific, exclusive group-specific, inclusive group-specific, and quasi-group probes with different specificities were selected, and all those probes together greatly increase the gene coverage. For data analysis, three strategies have been implemented. First, a universal standard has been implemented so that data normalization and comparison of samples from different sites, time points, or laboratories can be conducted. Second, a genomic standard is used to quantitatively analyze gene abundance. Third, a software package (including databases) has been developed for sequence retrieval, probe design, information storage, and especially, data analysis and automatic update, which greatly facilitate the management and analysis of complicated GeoChip data sets. GeoChip 3.0 has been used for analyses of responses of microbial communities to elevated CO2 and increased temperature. The results showed that autotrophic CO2 and N2 fixation by microorganisms increased significantly in response to elevated CO2. This also demonstrates that GeoChip can provide insights into biogeochemical processes and functional activities of microbial communities important to human health, agriculture, energy, global climate change, ecosystem management, and environmental cleanup and restoration. It is also particularly useful for providing direct linkages of microbial genes/populations to ecosystem processes and functions.

Published
2009

3. Impact of prescribed fire on soil microbial communities in a Southern Appalachian Forest clear-cut.

Author

Rafie, S. A. A., Blentlinger, L. R., Putt, A. D., Williams, D. E., Joyner, D. C., Campa, M. F., Schubert, M. J., Hoyt, K. P., Horn, S. P., Franklin, J. A., and Hazen, T. C.

Subjects
PRESCRIBED burning, MICROBIAL communities, FOREST management, MIXED forests, TEMPERATE forests, SOIL microbial ecology
Abstract

Escalating wildfire frequency and severity, exacerbated by shifting climate patterns, pose significant ecological and economic challenges. Prescribed burns, a common forest management tool, aim to mitigate wildfire risks and protect biodiversity. Nevertheless, understanding the impact of prescribed burns on soil and microbial communities in temperate mixed forests, considering temporal dynamics and slash fuel types, remains crucial. Our study, conducted at the University of Tennessee Forest Resources AgResearch and Education Center in Oak Ridge, TN, employed controlled burns across various treatments, and the findings indicate that low-intensity prescribed burns have none or minimal short-term effects on soil parameters but may alter soil nutrient concentrations, as evidenced by significant changes in porewater acetate, formate, and nitrate concentrations. These burns also induce shifts in microbial community structure and diversity, with Proteobacteria and Acidobacteria increasing significantly post-fire, possibly aiding soil recovery. In contrast, Verrucomicrobia showed a notable decrease over time, and other specific microbial taxa correlated with soil pH, porewater nitrate, ammonium, and phosphate concentrations. Our research contributes to understanding the intricate relationships between prescribed fire, soil dynamics, and microbial responses in temperate mixed forests in the Southern Appalachian Region, which is valuable for informed land management practices in the face of evolving environmental challenges. [ABSTRACT FROM AUTHOR]

Published
2024
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17. Generalized Schemes for High-Throughput Manipulation of the Desulfovibrio vulgaris Genome

Author

Chhabra, S. R., primary, Butland, G., additional, Elias, D. A., additional, Chandonia, J.-M., additional, Fok, O.-Y., additional, Juba, T. R., additional, Gorur, A., additional, Allen, S., additional, Leung, C. M., additional, Keller, K. L., additional, Reveco, S., additional, Zane, G. M., additional, Semkiw, E., additional, Prathapam, R., additional, Gold, B., additional, Singer, M., additional, Ouellet, M., additional, Szakal, E. D., additional, Jorgens, D., additional, Price, M. N., additional, Witkowska, H. E., additional, Beller, H. R., additional, Arkin, A. P., additional, Hazen, T. C., additional, Biggin, M. D., additional, Auer, M., additional, Wall, J. D., additional, and Keasling, J. D., additional

Published
2011
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18. Colloid-based multiplexed screening for plant biomass-degrading glycoside hydrolase activities in microbial communities

Author

Reindl, W., primary, Deng, K., additional, Gladden, J. M., additional, Cheng, G., additional, Wong, A., additional, Singer, S. W., additional, Singh, S., additional, Lee, J.-C., additional, Yao, C.-H., additional, Hazen, T. C., additional, Singh, A. K., additional, Simmons, B. A., additional, Adams, P. D., additional, and Northen, T. R., additional

Published
2011
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26. Histopathology of red-sore disease (<em>Aeromonas hydrophila</em>) in naturally and experimentally infected largemouth bass <em>Micropterus salmoides</em> (Lacépède).

Author

Huizinga, H. W., Esch, G. W., and Hazen, T. C.

Subjects
HISTOPATHOLOGY, LYMPHOID tissue, LARGEMOUTH bass, BILIARY tract, BIOCHEMISTRY, MICROPTERUS
Abstract

The histopathology of rod-sore disease, caused by the gram-negative bacterium, Aeromonas hydrophila, is described for largemouth bass, Micropterus salmoides. Externally, lesions range from those affecting a few scales (pin-point), to those associated with extensive chronic ulcerations; there is focal haemorrhage, oedema and dermal necrosis which exposes underlying muscles producing infiltration of mononuclear and granulocytic inflammatory cells. Internally, the liver and kidneys are foci for toxic products produced by A. hydrophila with, in the most severe cases, complete destruction of the structural integrity of both organs. Pathological changes were not serious in either the spleen or heart, even in cases with massive damage in the liver and kidney. Internal and external lesions were similar in both natural and experimentally induced infections. The pathobiology of red-sore disease in bass is postulated to be linked to elevated water temperature stimulating increased metabolism, decreased body condition and stress, leading to the increased production of corticosteroids and the concomitant rise in susceptibility to infection. [ABSTRACT FROM AUTHOR]

Published
1979
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32. Comparison of multiple ecogenomics methods for determining ecosystem function in uranium-contaminated environments

Author

Hazen, T. C., Dehal, P., Aikin, A. P., Fields, M. W., Keller, M., Zhou, J., Gary Andersen, Brodie, F. L., Wyborski, D. L., Abulencia, C. B., Hemme, C. L., Gentry, T., Watson, D. B., and Richardson, P.

Subjects
Earth Sciences
Abstract

Background: Bioremediation may offer the only feasible strategy for the nearly intractable problem of metal and radionuclide contamination of soil and groundwater. To understand bioremediation in contaminated environments, it is critical to determine the organisms present in these environments, analyze their responses to stress conditions, and elucidate functional position in the environment. Methods: We used multiple molecular techniques on both sediment and groundwater to develop a better understanding of the functional capability and stress level within the microbial community in relationship to over one hundred geochemical parameters. Due to the low pH (3.5-4.5) and high contaminant levels (e.g., uranium) microbial densities and activities were low. We used a phage polymerase amplification system to construct large and small insert DNA libraries, performed metagenome sequencing, constructed clonal libraries of select functional genes (SSU rRNA gene, nirK, nirS, amoA, pmoA, and dsrAB), used a SSU rDNA Phylochip microarray (9,000 taxa), and a functional gene array (23K genes). A complete comparison for community differences and similarities between the different techniques was assessed using several bioinformatics techniques. Results: SSU rDNA analysis revealed the presence of distinct bacterial phyla, including proteobacteria, acidobacteria, and planctomycetes along the contaminant gradient. Metagenome analysis identified many of the same organisms, and diversity was lower in water than sediment. Analysis with functional gene arrays, phylochip, and specific probes for genes and organisms involved in biogeochemical cycling of C, N, and S, metal resistance, stress response, and contaminant degradation suggested that the dominant species could be biostimulated during in situ uranium reduction. Several other findings of difference and similarities between methods are presented. Conclusion: These systems biology field studies could be enabling for strategies to attenuate nletal and radionuclide contamination.

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