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

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.

[1]  Anders F. Andersson,et al.  Virus Population Dynamics and Acquired Virus Resistance in Natural Microbial Communities , 2008, Science.

[2]  Vincent J. Denef,et al.  Strain-resolved community proteomics reveals recombining genomes of acidophilic bacteria , 2007, Nature.

[3]  S. Kimura,et al.  Macroscopic Streamer Growths in Acidic, Metal-Rich Mine Waters in North Wales Consist of Novel and Remarkably Simple Bacterial Communities , 2006, Applied and Environmental Microbiology.

[4]  J. Banfield,et al.  Community Proteomics of a Natural Microbial Biofilm , 2005, Science.

[5]  L. T. Angenent,et al.  Molecular identification of potential pathogens in water and air of a hospital therapy pool. , 2005, Proceedings of the National Academy of Sciences of the United States of America.

[6]  J. Banfield,et al.  Metabolically Active Eukaryotic Communities in Extremely Acidic Mine Drainage , 2004, Applied and Environmental Microbiology.

[7]  J. Banfield,et al.  Acid mine drainage biogeochemistry at Iron Mountain, California , 2004, Geochemical transactions.

[8]  K. Schleifer,et al.  ARB: a software environment for sequence data. , 2004, Nucleic acids research.

[9]  J. Banfield,et al.  Community structure and metabolism through reconstruction of microbial genomes from the environment , 2004, Nature.

[10]  D. Johnson,et al.  Grazing of acidophilic bacteria by a flagellated protozoan , 2004, Microbial Ecology.

[11]  T. Stoeck,et al.  Novel Eukaryotes from the Permanently Anoxic Cariaco Basin (Caribbean Sea) , 2003, Applied and Environmental Microbiology.

[12]  J. Banfield,et al.  Extremely Acidophilic Protists from Acid Mine Drainage Host Rickettsiales-Lineage Endosymbionts That Have Intervening Sequences in Their 16S rRNA Genes , 2003, Applied and Environmental Microbiology.

[13]  J. Henson,et al.  Detection of Naegleria sp. in a Thermal, Acidic Stream in Yellowstone National Park , 2003, The Journal of eukaryotic microbiology.

[14]  Jillian F Banfield,et al.  Microbial communities in acid mine drainage. , 2003, FEMS microbiology ecology.

[15]  M. Sogin,et al.  From Genes to Genomes: Beyond Biodiversity in Spain’s Rio Tinto , 2003, The Biological Bulletin.

[16]  Harald Huber,et al.  In Situ Accessibility of Small-Subunit rRNA of Members of the Domains Bacteria, Archaea, and Eucarya to Cy3-Labeled Oligonucleotide Probes , 2003, Applied and Environmental Microbiology.

[17]  V. de Lorenzo,et al.  Testing the limits of biological tolerance to arsenic in a fungus isolated from the River Tinto. , 2003, Environmental microbiology.

[18]  Purificación López-García,et al.  Autochthonous eukaryotic diversity in hydrothermal sediment and experimental microcolonizers at the Mid-Atlantic Ridge , 2003, Proceedings of the National Academy of Sciences of the United States of America.

[19]  N. Pace,et al.  Culture-Independent Molecular Analysis of Microbial Constituents of the Healthy Human Outer Ear , 2003, Journal of Clinical Microbiology.

[20]  N. Pace,et al.  Novel kingdom-level eukaryotic diversity in anoxic environments , 2002, Proceedings of the National Academy of Sciences of the United States of America.

[21]  M. Sogin,et al.  Benthic eukaryotic diversity in the Guaymas Basin hydrothermal vent environment , 2002, Proceedings of the National Academy of Sciences of the United States of America.

[22]  M. Sogin,et al.  Microbiology: Eukaryotic diversity in Spain's River of Fire , 2002, Nature.

[23]  J. Banfield,et al.  Phylogeny of Microorganisms Populating a Thick, Subaerial, Predominantly Lithotrophic Biofilm at an Extreme Acid Mine Drainage Site , 2000, Applied and Environmental Microbiology.

[24]  Jillian F. Banfield,et al.  Seasonal Variations in Microbial Populations and Environmental Conditions in an Extreme Acid Mine Drainage Environment , 1999, Applied and Environmental Microbiology.

[25]  Thomas L. Madden,et al.  Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. , 1997, Nucleic acids research.

[26]  D. Johnson,et al.  Effects of acidophilic protozoa on populations of metal-mobilizing bacteria during the leaching of pyritic coal , 1993 .