Ecophysiology of Fe-Cycling Bacteria in Acidic Sediments

Abstract

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.