Ecophysiology of Fe-cycling bacteria in acidic sediments

Abstract

Using a combination of cultivation-dependent and -independent methods, this study aimed to elucidate the diversity of microorganisms involved in iron cycling and to resolve their in situ functional links in sediments of an acidic lignite mine lake. Using six different media with pH values ranging from 2.5 to 4.3, 117 isolates were obtained that grouped into 38 different strains, including 27 putative new species with respect to the closest characterized strains. Among the isolated strains, 22 strains were able to oxidize Fe(II), 34 were able to reduce Fe(III) in schwertmannite, the dominant iron oxide in this lake, and 21 could do both. All isolates falling into the Gammaproteobacteria (an unknown Dyella-like genus and Acidithiobacillus-related strains) were obtained from the top acidic sediment zones (pH 2.8). Firmicutes strains (related to Bacillus and Alicyclobacillus) were only isolated from deep, moderately acidic sediment zones (pH 4 to 5). Of the Alphaproteobacteria, Acidocella-related strains were only isolated from acidic zones, whereas Acidiphilium-related strains were isolated from all sediment depths. Bacterial clone libraries generally supported and complemented these patterns. Geobacter-related clone sequences were only obtained from deep sediment zones, and Geobacter-specific quantitative PCR yielded 8 × 10(5) gene copy numbers. Isolates related to the Acidobacterium, Acidocella, and Alicyclobacillus genera and to the unknown Dyella-like genus showed a broad pH tolerance, ranging from 2.5 to 5.0, and preferred schwertmannite to goethite for Fe(III) reduction. This study highlighted the variety of acidophilic microorganisms that are responsible for iron cycling in acidic environments, extending the results of recent laboratory-based studies that showed this trait to be widespread among acidophiles.

FIG. 1.

Frequencies of bacterial (A) and archaeal (B) phylogenetic lineages detected in 16S rRNA gene clone libraries derived from sediment zones North I (BacI and ArcI) and North IV (BacIV and ArcIV) of a core obtained from the northern basin. Calculations were based on the total number of clones associated with phylotypes of sequenced representatives at the phylum or class level for Proteobacteria for Bacteria libraries and the family level for Archaea libraries.

FIG. 2.

Phylogenetic tree of Acidobacteriaceae-related sequences showing the close relationship of 16S rRNA gene clones obtained from sediment zones I and IV of a core obtained from the northern basin and of a strain isolated from sediment zone I of a core obtained from the deep central basin. GenBank sequence accession numbers are shown; sequences from this study are shown in boldface. The Archaea Methanosarcina barkeri (AJ012094) was used as an out-group. Scale bar shows 0.1 change per nucleotide position.

FIG. 3.

Phylogenetic tree of Alphaproteobacteria-related sequences showing the close relationship of 16S rRNA gene clones obtained from sediment zones I and IV of a core obtained from the northern basin and of the strains isolated from sediment zones I and IV of cores obtained from the northern and deep central basin. GenBank sequence accession numbers are shown; sequences from this study are shown in boldface. The Gammaproteobacteria Escherichia coli (AF233451) was used as an out-group. Scale bar shows 0.1 change per nucleotide position.

FIG. 4.

Schematic of the key microbial players involved in Fe cycling in the acidic lignite mine Lake 77 ecosystem. Microbial players detected by isolation and 16S rRNA gene cloning included Fe(II) oxidizers and Fe(III) reducers. The oxygen content declined sharply to 0 at 2 to 10 mm below the water-sediment interface, and the pH increased from 3 in the water and the top sediment zone I to ca. 5 in zone IV.