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9. Genome Project Standards in a New Era of Sequencing

Author

Genomic Standards Consortium Human Microbiome Project Jumpstart Consortium, Chain, P. S. G., Grafham, D. V., Fulton, R. S., FitzGerald, M. G., Hostetler, J., Muzny, D., Ali, J., Birren, B., Bruce, D. C., Buhay, C., Cole, J. R., Ding, Y., Dugan, S., Field, D., Garrity, G. M., Gibbs, R., Graves, T., Han, C. S., Harrison, S. H., Highlander, S., Hugenholtz, P., Khouri, H. M., Kodira, C. D., Kolker, E., Kyrpides, N. C., Lang, D., Lapidus, A., Malfatti, S. A., Markowitz, V., Metha, T., Nelson, K. E., Parkhill, J., Pitluck, S., Qin, X., Read, T. D., Schmutz, J., Sozhamannan, S., Sterk, P., Strausberg, R. L., Sutton, G., Thomson, N. R., Tiedje, J. M., Weinstock, G., Wollam, A., and Detter, J. C.

Published
2009
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14. Genome Project Standards in a New Era of Sequencing

Author

Chain, P. S. G., Grafham, D. V., Fulton, R. S., FitzGerald, M. G., Hostetler, J., Muzny, D., Ali, J., Birren, B., Bruce, D. C., Buhay, C., Cole, J. R., Ding, Y., Dugan, S., Field, D., Garrity, G. M., Gibbs, R., Graves, T., Han, C. S., Harrison, S. H., Highlander, S., Hugenholtz, P., Khouri, H. M., Kodira, C. D., Kolker, E., Kyrpides, N. C., Lang, D., Lapidus, A., Malfatti, S. A., Markowitz, V., Metha, T., Nelson, K. E., Parkhill, J., Pitluck, S., Qin, X., Read, T. D., Schmutz, J., Sozhamannan, S., Sterk, P., Strausberg, R. L., Sutton, G., Thomson, N. R., Tiedje, J. M., Weinstock, G., Wollam, A., and Detter, J. C.

Published
2009

24. Global diversity and biogeography of bacterial communities in wastewater treatment plants

Author

Wu, L. W., Ning, D. L., Zhang, B., Li, Y., Zhang, P., Shan, X. Y., Zhang, Q. T., Brown, M., Li, Z. X., Van Nostrand, J. D., Ling, F. Q., Xiao, N. J., Zhang, Y., Vierheilig, J., Wells, G. F., Yang, Y. F., Deng, Y., Tu, Q. C., Wang, A. J., Zhang, T., He, Z. L., Keller, J., Nielsen, P. H., Alvarez, P. J. J., Criddle, C. S., Wagner, M., Tiedje, J. M., He, Q., Curtis, T. P., Stahl, D. A., Alvarez-Cohen, L., Rittmann, B. E., Wen, X. H., Zhou, J. Z., Cabrol, Léa (collab.), and Global Water Microbiome Consortium

Abstract

Microorganisms in wastewater treatment plants (WWTPs) are essential for water purification to protect public and environmental health. However, the diversity of microorganisms and the factors that control it are poorly understood. Using a systematic global-sampling effort, we analysed the 16S ribosomal RNA gene sequences from similar to 1,200 activated sludge samples taken from 269 WWTPs in 23 countries on 6 continents. Our analyses revealed that the global activated sludge bacterial communities contain similar to 1 billion bacterial phylotypes with a Poisson lognormal diversity distribution. Despite this high diversity, activated sludge has a small, global core bacterial community (n = 28 operational taxonomic units) that is strongly linked to activated sludge performance. Meta-analyses with global datasets associate the activated sludge microbiomes most closely to freshwater populations. In contrast to macroorganism diversity, activated sludge bacterial communities show no latitudinal gradient. Furthermore, their spatial turnover is scale-dependent and appears to be largely driven by stochastic processes (dispersal and drift), although deterministic factors (temperature and organic input) are also important. Our findings enhance our mechanistic understanding of the global diversity and biogeography of activated sludge bacterial communities within a theoretical ecology framework and have important implications for microbial ecology and wastewater treatment processes.

Published
2019

25. A new version of the RDP (Ribosomal Database Project)

Author

Maidak, B. L, Cole, J. R, Parker, C. T. Jr, Garrity, G. M, Larsen, N, Li, B, Lilburn, T. G, McCaughey, M. J, Olsen, G. J, Overbeek, R, Pramanik, S, Schmidt, T. M, Tiedje, J. M, and Woese, C. R

Subjects
Exobiology
Abstract

The Ribosomal Database Project (RDP-II), previously described by Maidak et al. [ Nucleic Acids Res. (1997), 25, 109-111], is now hosted by the Center for Microbial Ecology at Michigan State University. RDP-II is a curated database that offers ribosomal RNA (rRNA) nucleotide sequence data in aligned and unaligned forms, analysis services, and associated computer programs. During the past two years, data alignments have been updated and now include >9700 small subunit rRNA sequences. The recent development of an ObjectStore database will provide more rapid updating of data, better data accuracy and increased user access. RDP-II includes phylogenetically ordered alignments of rRNA sequences, derived phylogenetic trees, rRNA secondary structure diagrams, and various software programs for handling, analyzing and displaying alignments and trees. The data are available via anonymous ftp (ftp.cme.msu. edu) and WWW (http://www.cme.msu.edu/RDP). The WWW server provides ribosomal probe checking, approximate phylogenetic placement of user-submitted sequences, screening for possible chimeric rRNA sequences, automated alignment, and a suggested placement of an unknown sequence on an existing phylogenetic tree. Additional utilities also exist at RDP-II, including distance matrix, T-RFLP, and a Java-based viewer of the phylogenetic trees that can be used to create subtrees.

Published
1999
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26. Anaerobic processes in soil

Author

TIEDJE, J. M., SEXSTONE, A. J., PARKIN, T. B., REVSBECH, N. P., and SHELTON, D. R.

Published
1984

34. Using the class 1 integron-integrase gene as a proxy for anthropogenic pollution

Author

Civil and Environmental Engineering, Gillings, M. R., Gaze, W. H., Pruden, Amy, Smalla, K., Tiedje, J. M., Zhu, Y.-G., Civil and Environmental Engineering, Gillings, M. R., Gaze, W. H., Pruden, Amy, Smalla, K., Tiedje, J. M., and Zhu, Y.-G.

Abstract

Around all human activity, there are zones of pollution with pesticides, heavy metals, pharmaceuticals, personal care products and the microorganisms associated with human waste streams and agriculture. This diversity of pollutants, whose concentration varies spatially and temporally, is a major challenge for monitoring. Here, we suggest that the relative abundance of the clinical class 1 integron-integrase gene, intI1, is a good proxy for pollution because: (1) intI1 is linked to genes conferring resistance to antibiotics, disinfectants and heavy metals; (2) it is found in a wide variety of pathogenic and nonpathogenic bacteria; (3) its abundance can change rapidly because its host cells can have rapid generation times and it can move between bacteria by horizontal gene transfer; and (4) a single DNA sequence variant of intI1 is now found on a wide diversity of xenogenetic elements, these being complex mosaic DNA elements fixed through the agency of human selection. Here we review the literature examining the relationship between anthropogenic impacts and the abundance of intI1, and outline an approach by which intI1 could serve as a proxy for anthropogenic pollution.

Published
2015

35. Microbial communities of the kanchenjunga mountains, nepal himalaya: factors affecting abundance, culturability and activity of the high-altitude cold-tolerant microbes

Author

Stres, Blaž, Philippot, Laurent, Tiedje J. M., James M., Mahne, Ivan, Agricultural Institute of Slovenia, Microbiologie, Institut National de la Recherche Agronomique (INRA)-Université de Bourgogne (UB), University of Michigan [Ann Arbor], University of Michigan System, University of Ljubljana, and ProdInra, Migration

Subjects
[SDV] Life Sciences [q-bio], [SDE] Environmental Sciences, freeze thaw, [SDV]Life Sciences [q-bio], [SDE]Environmental Sciences, bacteria, respiration, soil
Published
2009

40. Anaerobic processes in soil

Author

Tiedje, J. M., primary, Sexstone, A. J., additional, Parkin, T. B., additional, Revsbech, N. P., additional, and Shelton, D. R., additional

Published
1984
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43. Fungal community structure in disease suppressive soils assessed by 28S LSU gene sequencing

Author

Penton, C. R., Gupta, V. V. S. R., Tiedje, J. M., Neate, S. M., Ophel-Keller, K., Gillings, M., Harvey, P., Pham, A., Roget, D. K., Penton, C. R., Gupta, V. V. S. R., Tiedje, J. M., Neate, S. M., Ophel-Keller, K., Gillings, M., Harvey, P., Pham, A., and Roget, D. K.

Abstract

Natural biological suppression of soil-borne diseases is a function of the activity and composition of soil microbial communities. Soil microbe and phytopathogen interactions can occur prior to crop sowing and/or in the rhizosphere, subsequently influencing both plant growth and productivity. Research on suppressive microbial communities has concentrated on bacteria although fungi can also influence soil-borne disease. Fungi were analyzed in co-located soils 'suppressive' or 'non-suppressive' for disease caused by Rhizoctonia solani AG 8 at two sites in South Australia using 454 pyrosequencing targeting the fungal 28S LSU rRNA gene. DNA was extracted from a minimum of 125 g of soil per replicate to reduce the micro-scale community variability, and from soil samples taken at sowing and from the rhizosphere at 7 weeks to cover the peak Rhizoctonia infection period. A total of ∼994,000 reads were classified into 917 genera covering 54% of the RDP Fungal Classifier database, a high diversity for an alkaline, low organic matter soil. Statistical analyses and community ordinations revealed significant differences in fungal community composition between suppressive and non-suppressive soil and between soil type/location. The majority of differences associated with suppressive soils were attributed to less than 40 genera including a number of endophytic species with plant pathogen suppression potentials and mycoparasites such as Xylaria spp. Non-suppressive soils were dominated by Alternaria , Gibberella and Penicillum. Pyrosequencing generated a detailed description of fungal community structure and identified candidate taxa that may influence pathogen-plant interactions in stable disease suppression. © 2014 Penton et al.

Published
2014

45. ENVIRONMENTAL ASSESSMENT OF TRIFLUOROACETIC ACID

Author

BOUTONNET J. C., Ed, Bringham, P, Calamari, DAVIDE ANDREA, DE ROOIJ, C, Franklin, J, Kawano, T, Libre, Jm, Mcculloch, A, Malinverno, G, Odom, J. M., Rush, G. M., Smythe, K, Sobolev, I, Thompson, R, and Tiedje, J. M.

Published
1999

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