Note to users. If you're seeing this message, it means that your browser cannot find this page's style/presentation instructions -- or possibly that you are using a browser that does not support current Web standards. Find out more about why this message is appearing, and what you can do to make your experience of our site the best it can be.

Science 26 August 2005:
Vol. 309. no. 5739, pp. 1387 - 1390
DOI: 10.1126/science.1112665
Prev | Table of Contents | Next

Reports

Computational Improvements Reveal Great Bacterial Diversity and High Metal Toxicity in Soil

Jason Gans, Murray Wolinsky, John Dunbar

The complexity of soil bacterial communities has thus far confounded effective measurement. However, with improved analytical methods, we show that the abundance distribution and total diversity can be deciphered. Reanalysis of reassociation kinetics for bacterial community DNA from pristine and metal-polluted soils showed that a power law best described the abundance distributions. More than one million distinct genomes occurred in the pristine soil, exceeding previous estimates by two orders of magnitude. Metal pollution reduced diversity more than 99.9%, revealing the highly toxic effect of metal contamination, especially for rare taxa.

Bioscience Division, Los Alamos National Laboratory, Los Alamos, NM 87501, USA.

Read the Full Text


THIS ARTICLE HAS BEEN CITED BY OTHER ARTICLES:
Pyrosequencing-Based Assessment of Soil pH as a Predictor of Soil Bacterial Community Structure at the Continental Scale.
C. L. Lauber, M. Hamady, R. Knight, and N. Fierer (2009)
Appl. Envir. Microbiol. 75, 5111-5120
   Abstract »    Full Text »    PDF »
ESPRIT: estimating species richness using large collections of 16S rRNA pyrosequences.
Y. Sun, Y. Cai, L. Liu, F. Yu, M. L. Farrell, W. McKendree, and W. Farmerie (2009)
Nucleic Acids Res. 37, e76
   Abstract »    Full Text »    PDF »
Selection of Sphingomonadaceae at the Base of Laccaria proxima and Russula exalbicans Fruiting Bodies.
F. G. H. Boersma, J. A. Warmink, F. A. Andreote, and J. D. van Elsas (2009)
Appl. Envir. Microbiol. 75, 1979-1989
   Abstract »    Full Text »    PDF »
Building communities one bacterium at a time.
D. B. Weibel (2008)
PNAS 105, 18075-18076
   Full Text »    PDF »
Colloquium Paper: Resistance, resilience, and redundancy in microbial communities.
S. D. Allison and J. B. H. Martiny (2008)
PNAS 105, 11512-11519
   Abstract »    Full Text »    PDF »
Cultivation of Hard-To-Culture Subsurface Mercury-Resistant Bacteria and Discovery of New merA Gene Sequences.
L. D. Rasmussen, C. Zawadsky, S. J. Binnerup, G. Oregaard, S. J. Sorensen, and N. Kroer (2008)
Appl. Envir. Microbiol. 74, 3795-3803
   Abstract »    Full Text »    PDF »
Coexistence of Antibiotic-Producing and Antibiotic-Sensitive Bacteria in Biofilms Is Mediated by Resistant Bacteria.
N. Narisawa, S. Haruta, H. Arai, M. Ishii, and Y. Igarashi (2008)
Appl. Envir. Microbiol. 74, 3887-3894
   Abstract »    Full Text »    PDF »
Identifying the fundamental units of bacterial diversity: A paradigm shift to incorporate ecology into bacterial systematics.
A. Koeppel, E. B. Perry, J. Sikorski, D. Krizanc, A. Warner, D. M. Ward, A. P. Rooney, E. Brambilla, N. Connor, R. M. Ratcliff, et al. (2008)
PNAS 105, 2504-2509
   Abstract »    Full Text »    PDF »
Global change tipping points: above- and below-ground biotic interactions in a low diversity ecosystem.
D. H Wall (2007)
Phil Trans R Soc B 362, 2291-2306
   Abstract »    Full Text »    PDF »
Metagenomic and Small-Subunit rRNA Analyses Reveal the Genetic Diversity of Bacteria, Archaea, Fungi, and Viruses in Soil.
N. Fierer, M. Breitbart, J. Nulton, P. Salamon, C. Lozupone, R. Jones, M. Robeson, R. A. Edwards, B. Felts, S. Rayhawk, et al. (2007)
Appl. Envir. Microbiol. 73, 7059-7066
   Abstract »    Full Text »    PDF »
Effects of Plant Biomass, Plant Diversity, and Water Content on Bacterial Communities in Soil Lysimeters: Implications for the Determinants of Bacterial Diversity.
D. Zul, S. Denzel, A. Kotz, and J. Overmann (2007)
Appl. Envir. Microbiol. 73, 6916-6929
   Abstract »    Full Text »    PDF »
PhylArray: phylogenetic probe design algorithm for microarray.
C. Militon, S. Rimour, M. Missaoui, C. Biderre, V. Barra, D. Hill, A. Mone, G. Gagne, H. Meier, E. Peyretaillade, et al. (2007)
Bioinformatics 23, 2550-2557
   Abstract »    Full Text »    PDF »
Interpreting Ecological Diversity Indices Applied to Terminal Restriction Fragment Length Polymorphism Data: Insights from Simulated Microbial Communities.
C. B. Blackwood, D. Hudleston, D. R. Zak, and J. S. Buyer (2007)
Appl. Envir. Microbiol. 73, 5276-5283
   Abstract »    Full Text »    PDF »
Antibiotics as signalling molecules.
G. Yim, H. Huimi Wang, and J. Davies FRS (2007)
Phil Trans R Soc B 362, 1195-1200
   Abstract »    Full Text »    PDF »
Serial Analysis of rRNA Genes and the Unexpected Dominance of Rare Members of Microbial Communities.
M. N. Ashby, J. Rine, E. F. Mongodin, K. E. Nelson, and D. Dimster-Denk (2007)
Appl. Envir. Microbiol. 73, 4532-4542
   Abstract »    Full Text »    PDF »
Global patterns in bacterial diversity.
C. A. Lozupone and R. Knight (2007)
PNAS 104, 11436-11440
   Abstract »    Full Text »    PDF »
Atmospheric Movement of Microorganisms in Clouds of Desert Dust and Implications for Human Health.
D. W. Griffin (2007)
Clin. Microbiol. Rev. 20, 459-477
   Abstract »    Full Text »    PDF »
Geographical Distribution and Diversity of Bacteria Associated with Natural Populations of Drosophila melanogaster.
V. Corby-Harris, A. C. Pontaroli, L. J. Shimkets, J. L. Bennetzen, K. E. Habel, and D. E. L. Promislow (2007)
Appl. Envir. Microbiol. 73, 3470-3479
   Abstract »    Full Text »    PDF »
Advanced sequencing technologies and their wider impact in microbiology.
N. Hall (2007)
J. Exp. Biol. 210, 1518-1525
   Abstract »    Full Text »    PDF »
Isolation and Characterization of Soil Bacteria That Define Terriglobus gen. nov., in the Phylum Acidobacteria.
S. A. Eichorst, J. A. Breznak, and T. M. Schmidt (2007)
Appl. Envir. Microbiol. 73, 2708-2717
   Abstract »    Full Text »    PDF »
Measuring Species Richness Based on Microbial Community Fingerprints: the Emperor Has No Clothes.
S. J. Bent, J. D. Pierson, L. J. Forney, R. Danovaro, G. M. Luna, A. Dell'Anno, and B. Pietrangeli (2007)
Appl. Envir. Microbiol. 73, 2399-2401
   Full Text »    PDF »
Soil Microbial Community Analysis Using Denaturing Gradient Gel Electrophoresis.
C. H. Nakatsu (2007)
Soil Sci. Soc. Am. J. 71, 562-571
   Abstract »    Full Text »    PDF »
Soil Microbial Community Analysis using Terminal Restriction Fragment Length Polymorphisms.
J. E. Thies (2007)
Soil Sci. Soc. Am. J. 71, 579-591
   Abstract »    Full Text »    PDF »
DNA Sequencing: Strategies for Soil Microbiology.
M. D. Zwolinski (2007)
Soil Sci. Soc. Am. J. 71, 592-600
   Abstract »    Full Text »    PDF »
Urban aerosols harbor diverse and dynamic bacterial populations.
E. L. Brodie, T. Z. DeSantis, J. P. M. Parker, I. X. Zubietta, Y. M. Piceno, and G. L. Andersen (2007)
PNAS 104, 299-304
   Abstract »    Full Text »    PDF »
Towards a conceptual and operational union of bacterial systematics, ecology, and evolution.
F. M Cohan (2006)
Phil Trans R Soc B 361, 1985-1996
   Abstract »    Full Text »    PDF »
Patterns and mechanisms of genetic and phenotypic differentiation in marine microbes.
M. F Polz, D. E Hunt, S. P Preheim, and D. M Weinreich (2006)
Phil Trans R Soc B 361, 2009-2021
   Abstract »    Full Text »    PDF »
What is the extent of prokaryotic diversity?.
T. P Curtis, I. M Head, M. Lunn, S. Woodcock, P. D Schloss, and W. T Sloan (2006)
Phil Trans R Soc B 361, 2023-2037
   Abstract »    Full Text »    PDF »
Accurately quantifying low-abundant targets amid similar sequences by revealing hidden correlations in oligonucleotide microarray data.
L. A. Marcelino, V. Backman, A. Donaldson, C. Steadman, J. R. Thompson, S. P. Preheim, C. Lien, E. Lim, D. Veneziano, and M. F. Polz (2006)
PNAS 103, 13629-13634
   Abstract »    Full Text »    PDF »
Comment on "Computational Improvements Reveal Great Bacterial Diversity and High Metal Toxicity in Soil".
I. Volkov, J. R. Banavar, and A. Maritan (2006)
Science 313, 918a
   Abstract »    Full Text »    PDF »
Response to Comment by Volkov et al. on "Computational Improvements Reveal Great Bacterial Diversity and High Metal Toxicity in Soil".
J. Gans, M. Wolinsky, and J. Dunbar (2006)
Science 313, 918b
   Abstract »    Full Text »    PDF »
Comment on "Computational Improvements Reveal Great Bacterial Diversity and High Metal Toxicity in Soil".
J. Bunge, S. S. Epstein, and D. G. Peterson (2006)
Science 313, 918c
   Abstract »    Full Text »    PDF »
Response to Comment by Bunge et al. on "Computational Improvements Reveal Great Bacterial Diversity and High Metal Toxicity in Soil".
J. Gans, M. Wolinsky, and J. Dunbar (2006)
Science 313, 918d
   Abstract »    Full Text »    PDF »
Diversity of planctomycetes in soil in relation to soil history and environmental heterogeneity..
D. H. Buckley, V. Huangyutitham, T. A. Nelson, A. Rumberger, and J. E. Thies (2006)
Appl. Envir. Microbiol. 72, 4522-4531
   Abstract »    Full Text »    PDF »
Identifying the Dominant Soil Bacterial Taxa in Libraries of 16S rRNA and 16S rRNA Genes..
P. H. Janssen (2006)
Appl. Envir. Microbiol. 72, 1719-1728
   Full Text »    PDF »
Predicting microbial species richness.
S.-H. Hong, J. Bunge, S.-O. Jeon, and S. S. Epstein (2006)
PNAS 103, 117-122
   Abstract »    Full Text »    PDF »


To Advertise     Find Products

Science. ISSN 0036-8075 (print), 1095-9203 (online)