Insights into the Diversity of Eukaryotes in Acid Mine Drainage Biofilm Communities

Baker, Brett J., Tyson, Gene W., Goosherst, Lindsey and Banfield, Jillian F. (2009) Insights into the Diversity of Eukaryotes in Acid Mine Drainage Biofilm Communities. Applied and Environmental Microbiology, 75 7: 2192-2199. doi:10.1128/AEM.02500-08

Attached Files (Some files may be inaccessible until you login with your UQ eSpace credentials)
Name Description MIMEType Size Downloads
UQ202672_OA.pdf Full text (open access) application/pdf 1.77MB 0

Author Baker, Brett J.
Tyson, Gene W.
Goosherst, Lindsey
Banfield, Jillian F.
Title Insights into the Diversity of Eukaryotes in Acid Mine Drainage Biofilm Communities
Journal name Applied and Environmental Microbiology   Check publisher's open access policy
ISSN 0099-2240
Publication date 2009-04-01
Year available 2009
Sub-type Article (original research)
DOI 10.1128/AEM.02500-08
Open Access Status File (Publisher version)
Volume 75
Issue 7
Start page 2192
End page 2199
Total pages 8
Editor L Nicholson Ornston
Place of publication United States
Publisher American Society for Microbiology
Collection year 2010
Language eng
Subject C1
Abstract Microscopic eukaryotes are known to have important ecosystem functions, but their diversity in most environments remains vastly unexplored. Here we analyzed an 18S rRNA gene library from a subsurface iron- and sulfur-oxidizing microbial community growing in highly acidic (pH < 0.9) runoff within the Richmond Mine at Iron Mountain (northern California). Phylogenetic analysis revealed that the majority (68%) of the sequences belonged to fungi. Protists falling into the deeply branching lineage named the acidophilic protist clade (APC) and the class Heterolobosea were also present. The APC group represents kingdom-level novelty, with <76% sequence similarity to 18S rRNA gene sequences of organisms from other environments. Fluorescently labeled oligonucleotide rRNA probes were designed to target each of these groups in biofilm samples, enabling abundance and morphological characterization. Results revealed that the populations vary significantly with the habitat and no group is ubiquitous. Surprisingly, many of the eukaryotic lineages (with the exception of the APC) are closely related to neutrophiles, suggesting that they recently adapted to this extreme environment. Molecular analyses presented here confirm that the number of eukaryotic species associated with the acid mine drainage (AMD) communities is low. This finding is consistent with previous results showing a limited diversity of archaea, bacteria, and viruses in AMD environments and suggests that the environmental pressures and interplay between the members of these communities limit species diversity at all trophic levels.
Keyword eukaryotes
microscopic eukaryotes
biofilm
References Altschul, S. F., T. L. Madden, A. A. Schaffer, J. Zhang, Z. Zhang, W. Miller, and D. J. Lipman. 1997. Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res. 25:3389-3402.[Abstract/Free Full Text]2 Amaral Zettler, L. A., F. Gómez, E. R. Zettler, B. G. Keenan, R. Amils, and M. L. Sogin. 2002. Eukaryotic diversity in Spain's river of fire. Nature 417:137.[CrossRef][Medline][Get it at UQ Library]3 Amaral Zettler, L. A., M. A. Messerli, A. D. Laatsch, P. J. S. Smith, and M. L. Sogin. 2003. From genes to genomes: beyond biodiversity in Spain's Rio Tinto. Biol. Bull. 204:205-209.[Abstract/Free Full Text]4 Andersson, A. F., and J. F. Banfield. 2008. Virus population dynamics and acquired virus resistance in natural microbial communities. Science 320:1047-1050.[Abstract/Free Full Text]5 Angenent, L. T., S. T. Kelley, A. S. Amand, N. R. Pace, and M. T. Hernandez. 2005. Molecular identification of potential pathogens in water and air of a hospital therapy pool. Proc. Natl. Acad. Sci. USA 102:4860-4865.[Abstract/Free Full Text]6 Baker, B. J., and J. F. Banfield. 2003. Microbial communities in acid mine drainage. FEMS Microb. Ecol. 44:1-14.[Medline][Get it at UQ Library]7 Baker, B. J., P. Hugenholtz, S. C. Dawson, and J. F. Banfield. 2003. Extremely acidophilic protists host Rickettsiales-lineage endosymbionts with an intervening sequence in their 16S rRNA genes. Appl. Environ. Microbiol. 69:5512-5518.[Abstract/Free Full Text]8 Baker, B. J., M. A. Lutz, S. C. Dawson, P. L. Bond, and J. F. Banfield. 2004. Metabolically active eukaryotes in extremely acidic mine drainage. Appl. Environ. Microbiol. 70:6264-6271.[Abstract/Free Full Text]9 Behrens, S., C. Ruhland, J. Inacio, H. Huber, A. Fonseca, I. Spencer-Martins, B. M. Fuchs, and R. Amann. 2003. In situ accessibility of small-subunit rRNA of members of the domains Bacteria, Archaea, and Eucarya to Cy3-labeled oligonucleotide probes. Appl. Environ. Microbiol. 69:1748-1758.[Abstract/Free Full Text]10 Bond, P. L., S. P. Smriga, and J. F. Banfield. 2000. Phylogeny of microorganisms populating a thick, subaerial, predominantly lithotrophic biofilm at an extreme acid mine drainage site. Appl. Environ. Microbiol. 66:3842-3849.[Abstract/Free Full Text]11 Cánovas, D., C. Durán, N. Rodriguez, R. Amils, and V. de Lorenzo. 2003. Testing the limits of biological tolerance to arsenic in a fungus isolate from the River Tinto. Environ. Microbiol. 5:133-138.[CrossRef][Medline][Get it at UQ Library]12 Dawson, S. C., and N. R. Pace. 2002. Novel kingdom-level eukaryotic diversity in anoxic environments. Proc. Natl. Acad. Sci. USA 99:8324-8329.[Abstract/Free Full Text]13 Druschel, G. K., B. J. Baker, T. M. Gihring, and J. F. Banfield. 2004. Biogeochemistry of acid mine drainage at Iron Mountain, California. Geochem. Trans. 5:13-32.[CrossRef][Get it at UQ Library]14 Edgcomb, V. P., D. T. Kysela, A. Teske, A. de Vera Gomez, and M. L. Sogin. 2002. Benthic eukaryotic diversity in the Guaymas Basin hydrothermal vent environment. Proc. Natl. Acad. Sci. USA 99:7658-7662.[Abstract/Free Full Text]15 Edwards, K. J., T. M. Gihring, and J. F. Banfield. 1999. Seasonal variations in microbial populations and environmental conditions in an extreme acid mine drainage environment. Appl. Environ. Microbiol. 65:3627-3632.[Abstract/Free Full Text]16 Frank, D. N., G. B. Spiegelman, W. Davis, E. Wagner, E. Lyons, and N. R. Pace. 2003. Culture-independent molecular analysis of microbial constituents of the healthy human outer ear. J. Clin. Microbiol. 41:295-303.[Abstract/Free Full Text]17 Hallberg, K. B., K. Coupland, S. Kimura, and D. B. Johnson. 2006. Macroscopic streamer growths in acidic, metal-rich mine waters in North Wales consist of novel and remarkably simple bacterial communities. Appl. Environ. Microbiol. 72:2022-2030.[Abstract/Free Full Text]18 Johnson, D. B., and L. Rang. 1993. Effects of acidophilic protozoa on populations of metal-mobilizing bacteria during the leaching of pyritic coal. J. Gen. Microbiol. 139:1417-1423.[Abstract/Free Full Text]19 Lo, I., V. J. Denef, N. C. Verberkmoes, M. B. Shah, D. Goltsman, G. DiBartolo, G. W. Tyson, E. E. Allen, R. J. Ram, J. C. Detter, P. Richardson, M. P. Thelen, R. L. Hettich, and J. F. Banfield. 2007. Strain-resolved community proteomics reveals recombining genomes of acidophilic bacteria. Nature 466:537-541.[Get it at UQ Library]20 Lopez-Garcia, P., H. Philippe, F. Gail, and D. Moreira. 2003. Autochthonous eukaryotic diversity in hydrothermal sediment and experimental microcolonizers at the Mid-Atlantic Ridge. Proc. Natl. Acad. Sci. USA 100:697-702.[Abstract/Free Full Text]21 Ludwig, W., O. Strunk, R. Westram, L. Richter, H. Meier, Yadhukumar, Arno Buchner, T. Lai, S. Steppi, G. Jobb, W. Förster, I. Brettske, S. Gerber, A. W. Ginhart, O. Gross, W. Grumann, S. Hermann, R. Jost, A. König, T. Liss, R. Lüßmann, M. May, B. Nonhoff, B. Reichel, R. Strehlow, A. Stamatakis, N. Stuckmann, A. Vilbig, M. Lenke, T. Ludwig, A. Bode, and K.-H. Schleifer. 2004. ARB: a software environment for sequence data. Nucleic Acids Res. 32:1363-1371.[Abstract/Free Full Text]22 McGinness, S., and D. B. Johnson. 1992. Grazing of acidophilic bacteria by a flagellated protozoan. Microb. Ecol. 23:75-86.[CrossRef][Get it at UQ Library]23 Ram, R. J., N. VerBerkmoes, M. P. Thelen, G. W. Tyson, B. J. Baker, M. Shah, R. C. Blake II, R. Hettich, and J. F. Banfield. 2005. Community proteomics of a natural microbial biofilm. Science 308:1915-1920.[Abstract/Free Full Text]24 Sheehan, K. B., M. J. Ferris, and J. M. Henson. 2003. Detection of Naegleria sp. in a thermal, acidic stream in Yellowstone National Park. J. Eukaryot. Microbiol. 50:263-265.[CrossRef][Medline][Get it at UQ Library]25 Stoeck, T., G. T. Taylor, and S. S. Epstein. 2003. Novel eukaryotes from the permanently anoxic cariaco basin (Caribbean Sea). Appl. Environ. Microbiol. 69:5656-5663.[Abstract/Free Full Text]26 Tyson, G. W., J. Chapman, P. Hugenholtz, E. E. Allen, R. J. Ram, P. M. Richarson, V. V. Solovyev, E. M. Rubin, D. S. Rokhsar, and J. F. Banfield. 2004. Community structure and metabolism through reconstruction of microbial genomes from the environment. Nature 428:37-43.[CrossRef][Medline][Get it at UQ Library]
Q-Index Code C1
Q-Index Status Confirmed Code
Additional Notes Published ahead of print on 6 February 2009

Document type: Journal Article
Sub-type: Article (original research)
Collections: 2010 Higher Education Research Data Collection
Advanced Water Management Centre Publications
 
Versions
Version Filter Type
Citation counts: TR Web of Science Citation Count  Cited 47 times in Thomson Reuters Web of Science Article | Citations
Scopus Citation Count Cited 50 times in Scopus Article | Citations
Google Scholar Search Google Scholar
Created: Tue, 13 Apr 2010, 21:36:29 EST by Hong Lee on behalf of Advanced Water Management Centre