Archaeal diversity in acid mine drainage from Dabaoshan Mine, China

143

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, Acidocellarelated 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. Geobacterrelated 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 laboratorybased studies that showed this trait to be widespread among acidophiles.

Section: Discussioncontrasting

confidence: 45%

Ecophysiology of Fe-Cycling Bacteria in Acidic Sediments

Gischkat

Reiche

et al. 2010

143

“…AMD is a prevalent, international environmental problem that threatens aquatic life and surrounding ecosystems (11,15,21,24,26,33,43,44), although it also has been regarded as an excellent model to investigate linkages between microbial communities and geochemistry because of its relatively simple microbial community composition and structure (5,6,8). A better understanding of the microbial community diversity and ecology in AMD would provide a scientific foundation not only for the bioremediation of AMD-contaminated environments but also for potential applications for the energy-efficient recovery of valuable metals from mine waste and the removal of sulfur from coal (6, 23).The phylogenetic diversity of AMD microbial communities has been well studied by 16S rRNA-based approaches, including PCR cloning (36,54,55,57), denaturing gradient gel electrophoresis (DGGE) (10,20,21), fluorescence in situ hybridization (9,29,40), and oligonucleotide microarrays (14, 56). For instance, the DNA sequencing of a natural acidophilic biofilm (pH 0.80) revealed that pathways for carbon and nitrogen fixation and energy generation might occur in these communities and provided insight into survival strategies in such an extreme environment (45).…”

mentioning

confidence: 99%

“…The phylogenetic diversity of AMD microbial communities has been well studied by 16S rRNA-based approaches, including PCR cloning (36,54,55,57), denaturing gradient gel electrophoresis (DGGE) (10,20,21), fluorescence in situ hybridization (9,29,40), and oligonucleotide microarrays (14, 56). For instance, the DNA sequencing of a natural acidophilic biofilm (pH 0.80) revealed that pathways for carbon and nitrogen fixation and energy generation might occur in these communities and provided insight into survival strategies in such an extreme environment (45).…”

mentioning

confidence: 99%

GeoChip-Based Analysis of the Functional Gene Diversity and Metabolic Potential of Microbial Communities in Acid Mine Drainage

Xie

Liu

et al. 2011

Acid mine drainage (AMD) is an extreme environment, usually with low pH and high concentrations of metals. Although the phylogenetic diversity of AMD microbial communities has been examined extensively, little is known about their functional gene diversity and metabolic potential. In this study, a comprehensive functional gene array (GeoChip 2.0) was used to analyze the functional diversity, composition, structure, and metabolic potential of AMD microbial communities from three copper mines in China. GeoChip data indicated that these microbial communities were functionally diverse as measured by the number of genes detected, gene overlapping, unique genes, and various diversity indices. Almost all key functional gene categories targeted by GeoChip 2.0 were detected in the AMD microbial communities, including carbon fixation, carbon degradation, methane generation, nitrogen fixation, nitrification, denitrification, ammonification, nitrogen reduction, sulfur metabolism, metal resistance, and organic contaminant degradation, which suggested that the functional gene diversity was higher than was previously thought. Mantel test results indicated that AMD microbial communities are shaped largely by surrounding environmental factors (e.g., S, Mg, and Cu). Functional genes (e.g., narG and norB) and several key functional processes (e.g., methane generation, ammonification, denitrification, sulfite reduction, and organic contaminant degradation) were significantly (P < 0.10) correlated with environmental variables. This study presents an overview of functional gene diversity and the structure of AMD microbial communities and also provides insights into our understanding of metabolic potential in AMD ecosystems.When sulfide ores are exposed to air, water, and microbes (autotrophic and heterotrophic archaea and bacteria) during the exploration of coals and metal deposits, acid mine drainage (AMD), which usually has low pH and high concentrations of sulfate and metals, is formed (5,8,34,52). AMD is a prevalent, international environmental problem that threatens aquatic life and surrounding ecosystems (11,15,21,24,26,33,43,44), although it also has been regarded as an excellent model to investigate linkages between microbial communities and geochemistry because of its relatively simple microbial community composition and structure (5,6,8). A better understanding of the microbial community diversity and ecology in AMD would provide a scientific foundation not only for the bioremediation of AMD-contaminated environments but also for potential applications for the energy-efficient recovery of valuable metals from mine waste and the removal of sulfur from coal (6, 23).The phylogenetic diversity of AMD microbial communities has been well studied by 16S rRNA-based approaches, including PCR cloning (36,54,55,57), denaturing gradient gel electrophoresis (DGGE) (10,20,21), fluorescence in situ hybridization (9,29,40), and oligonucleotide microarrays (14, 56). For instance, the DNA sequencing of a natural acidophilic biofilm (pH 0.80)...

“…Detection or quantification of the Ferroplasmaceae in these environments was done mostly using small subunit (SSU) rRNA-targeting analyses, such as 16S rRNA gene clone libraries' sequencing, amplified rRNA gene restriction analysis (ARDRA) profiling, real-time quantitative PCR, restriction fragment length polymorphism (RFLP) or fluorescence in situ hybridization (FISH), and oligonucleotide microarray analysis, all of which revealed the presence of these archaea in a number of pyritic/arsenopyritic, gold-arsenopyritic/chalcopyritic, and lead-, zinc-, and copper-containing mines across all continents (11,24,26,45,46,51,55,56,57,58). Clones related to the family Ferroplasmaceae have also been documented in further natural sulfide-rich ecosystems, e.g., in the snottites, i.e., the stalactite-like formations of microbial origin taken from the walls of Frasassi Cave and in the Rio Garrafo cave systems, both located in Italy, where acidic microenvironments were formed as a result of sulfide oxidation (38).…”

mentioning

confidence: 99%

Environmental, Biogeographic, and Biochemical Patterns of Archaea of the Family Ferroplasmaceae

Golyshina

2011

About 10 years ago, a new family of cell wall-deficient, iron-oxidizing archaea, Ferroplasmaceae, within the large archaeal phylum Euryarchaeota, was described. In this minireview, I summarize the research progress achieved since then and report on the current status of taxonomy, biogeography, physiological diversity, biochemistry, and other research areas involving this exciting group of acidophilic archaea.Microorganisms thrive remarkably under various conditions, including high temperatures, extremely high osmosis, and very acidic pH, that would generally be considered hostile or limiting to higher organisms. Studying and understanding the uniqueness of extremophilic organisms and the biochemical and cellular processes underlying their functioning and role in biogeochemical processes comprise an emerging research area in modern bioscience. Of special interest for various biotechnological applications are enzymes produced by extremophiles, the so-called extremozymes, which exhibit a high activity and stability under extreme physical-chemical conditions. The representatives of the "third domain of life," the archaea, are unique contributors to this area of special interest. Several factors make the archaea an attractive subject of study, including their relatively recent history of discovery, ability (often much higher than that of bacteria) to adapt to harsh environments, enigmatic nature, and low cultivability.