TABLE 3.
Bacterial isolates from acidic lignite mine lake sediments using 6 different agarose overlay plates, with taxonomic status, identity values based on analysis of 16S rRNA gene sequences, and the results of microoxic and anoxic Fe(III) reduction experiments and Fe(II) oxidation capacities observed on Fe(II)-containing agarose overlay plates
| Representative straina | No. of isolatesb | Closest type strain (GenBank sequence accession no., % identity) | Fe-cycling capacity |
||||||
|---|---|---|---|---|---|---|---|---|---|
| Reported (reference[s])c | Oxidationd | Microoxic reductionf | Anoxic reductionf | ||||||
| YE3-D1-20 | 1 | Edaphobacter modestus Jbg-1T (DQ528760, 93.9) | UO, R (7, 25) | − (Feo) | + | + | |||
| YE4-D4-2-CH | 2 | Streptomyces ferralitis SFOp68T (AY262826, 98.4) | UO, UR | NAe | + | + | |||
| FeSo-D1-6-CH | 1 | Ferrimicrobium acidiphilum T23T (AF251436, 99.4) | O, R (36) | + | + | + | |||
| YE4-D4-16-CH | 1 | Actinocorallia aurea IFO 14752T (AB006177, 94.2) | UO, UR | − (FeTo) | + | (−) | |||
| YE4-D4-1-CH | 1 | Bacillus acidicola 105-2T (AF547209, 99.8) | UO, UR | NA | + | (−) | |||
| YE4-D4-4-CH | 1 | Bacillus pocheonensis Gsoil 420T (AB245377, 99) | UO, UR | − (FeTo) | + | (+) | |||
| YE3-D4-3i-CH | 2 | Alicyclobacillus contaminans 3-A191T (AB264026, 89.6) | O (37), UR | + (iFeo) | + | + | |||
| iFeo-D4-31-CH | 1 | Alicyclobacillus contaminans 3-A191T (AB264026, 90.6) | O, R (42) | + | − | + | |||
| YE3-D4-31i-CH | 3 | Alicyclobacillus ferrooxydans TC-34T (EU137838, 98.6) | O (72), UR | + (FeTo) | + | + | |||
| Feo-D4-16-CH | 1 | Alicyclobacillus ferrooxydans TC-34T (EU137838, 91.4) | O, R (42) | + | + | + | |||
| FeSo-D4-20-CH | 1 | Alicyclobacillus pomorum 3AT (AB089840, 91) | O (19), UR | + | + | (−) | |||
| FeSo-N4-1-CH | 2 | Alicyclobacillus tolerans K1T (AF137502, 95.1) | O (72), UR | + | + | + | |||
| YE4-D4-4i-CH | 2 | Alicyclobacillus tolerans K1T (AF137502, 94.9) | O (72), UR | + (FeTo) | + | + | |||
| Feo-N4-15-CH | 1 | Alicyclobacillus tolerans K1T (AF137502, 100) | O, R (46) | + | + | + | |||
| FeSo-N4-2-CH | 1 | Sulfobacillus acidophilus DSM 10332T (AB089842, 94.2) | O (58, 72), UR | − | + | + | |||
| FeSo-N4-3-CH | 1 | Sulfobacillus thermotolerans Kr1T (DQ124681, 99.1) | O, R (42) | + | + | + | |||
| FeSo-D1-15-CH | 1 | Acidiphilium acidophilum ATCC 27807T (D86511, 99.8) | UO, R (38) | − | + | + | |||
| YE3-D4-63i-CH | 1 | Acidiphilium acidophilum ATCC 27807T (D86511, 98.2) | UO, R (38) | NA | + | + | |||
| YE3-D1-35 | 1 | Acidiphilium cryptum ATCC 33463T (D30773, 100) | UO, R (6, 51) | NA | + | + | |||
| FeTo-D1-1-CH | 1 | Acidisphaera rubrifaciens HS-AP3T (D86512, 99.7) | UO, NR (15) | − | − | (−) | |||
| YE4-N1-5-CH | 2 | Acidocella facilis ATCC 35904T (D30774, 97) | UO, R (15) | − (FeTo) | + | + | |||
| FeTo-D4-17-CH | 1 | Methylocella tundrae T4T (AJ555244, 99.9) | UO, UR | + | − | (−) | |||
| YE3-D4-2i-CH | 1 | Methylocapsa acidiphila DSM 13967T (AJ278726, 98.6) | UO, UR | NA | (−) | (−) | |||
| YE4-D1-1-CH | 1 | Thiomonas cuprina NBRC 102094T (AB331953, 98.8) | UO, UR | − (FeTo) | + | − | |||
| YE3-D1-10-CH | 4 | Dyella yeojuensis R2A16-10T (DQ181549, 94.3) | O, R (15, 72) | + (FeTo) | + | + | |||
| FeSo-D1-9-CH | 1 | Acidithiobacillus ferrivorans NO-37T (AF376020, 99.4) | O, R (26) | + | + | (−) | |||
| FeSo-N1-1-CH | 1 | Acidithiobacillus ferrooxidans ATCC 23270T (AF465604, 99.3) | O, R (26) | + | + | (−) | |||
| FeTo-N1-3-CH | 1 | Acidithiobacillus ferrooxidans ATCC 23270T (AF465604, 99.5) | O, R (26) | − | + | (−) | |||
Strain designation was constructed as follows, by combining information about the medium, source, and isolate number separated by hyphens. The first part designates the medium type, the second part designates the origin of the sediment, e.g., D1 or D4 means deep site of the lake (D) and either upper sediment zone I (1) or deeper sediment zone IV (4). N1 or N4 means north shore site of the lake (N) and either upper sediment zone I (1) or deeper sediment zone IV (4). The next number is the sequential number of the isolate, and CH designates the presence of cycloheximide (CH) if it was added. The pHs of the media Feo, iFeo, FeSo, FeTo, YE3, and YE4 were 2.5, 2.5, 2.5, 4.3, 3.0, and 4.0, respectively. Strains which appear to be putative new species are presented in boldface.
A number greater than one indicates that isolates were grouped based on identical 16S rRNA gene sequences and colony morphologies on the plates.
Known Fe redox capacities of the closest cultivated strains based on the literature: O means Fe(II) oxidation; R means Fe(III) reduction; NO means no Fe(II) oxidation; NR means no Fe(III) reduction; UO means unknown for Fe(II) oxidation function; and UR means unknown for Fe(III) reduction.
Colonies from yeast extract media were checked for Fe(II) oxidation capacities on iron-rich media. +, positive for Fe(II) oxidation; −, negative for Fe(II) oxidation. The medium code in brackets indicates the iron-rich medium on which the colonies were able to grow.
NA, not applicable. Colonies from yeast extract media were tested for Fe(II) oxidation capacities on iron-rich media, but strains could not grow on the indicated medium.
+, Fe(II) formation in the liquid medium; −, no Fe(III) formation compared to uninoculated controls with cells growing in the medium; (−), tested, but no cell growth or Fe(III) formation was observed; (+), Fe(II) formation detected but not confirmed.