Microbial Iron Cycling in Acidic Geothermal Springs of Yellowstone National Park: Integrating Molecular Surveys, Geochemical Processes, and Isolation of Novel Fe-Active Microorganisms

Abstract

Geochemical, molecular, and physiological analyses of microbial isolates were combined to study the geomicrobiology of acidic iron oxide mats in Yellowstone National Park. Nineteen sampling locations from 11 geothermal springs were studied ranging in temperature from 53 to 88°C and pH 2.4 to 3.6. All iron oxide mats exhibited high diversity of crenarchaeal sequences from the Sulfolobales, Thermoproteales, and Desulfurococcales. The predominant Sulfolobales sequences were highly similar to Metallosphaera yellowstonensis str. MK1, previously isolated from one of these sites. Other groups of archaea were consistently associated with different types of iron oxide mats, including undescribed members of the phyla Thaumarchaeota and Euryarchaeota. Bacterial sequences were dominated by relatives of Hydrogenobaculum spp. above 65–70°C, but increased in diversity below 60°C. Cultivation of relevant iron-oxidizing and iron-reducing microbial isolates included Sulfolobus str. MK3, Sulfobacillus str. MK2, Acidicaldus str. MK6, and a new candidate genus in the Sulfolobales referred to as Sulfolobales str. MK5. Strains MK3 and MK5 are capable of oxidizing ferrous iron autotrophically, while strain MK2 oxidizes iron mixotrophically. Similar rates of iron oxidation were measured for M. yellowstonensis str. MK1 and Sulfolobales str. MK5. Biomineralized phases of ferric iron varied among cultures and field sites, and included ferric oxyhydroxides, K-jarosite, goethite, hematite, and scorodite depending on geochemical conditions. Strains MK5 and MK6 are capable of reducing ferric iron under anaerobic conditions with complex carbon sources. The combination of geochemical and molecular data as well as physiological observations of isolates suggests that the community structure of acidic Fe mats is linked with Fe cycling across temperatures ranging from 53 to 88°C.

Geoarchaeota: a new candidate phylum in the Archaea from high-temperature acidic iron mats in Yellowstone National Park

“…and Hydrogenobaculum spp. (Aquificales), as well as other less abundant, uncharacterized archaea and bacteria (Kozubal et al, 2012).…”

“…Contigs assigned to each replicate de novo assembly have similar G þ C content (%) and sequence read coverage that clearly distinguish them from other population clusters in this community (example shown in Supplementary Figure S1). Comparison of NAG1 sequence to reference databases (via blastp or blastn) revealed a consistent pattern (that is, poor sequence similarity to current reference genomes), and is clearly different than the other three to four predominant populations present in these systems (Kozubal et al, 2012). The assemblies were evaluated using NWF-PCA (Teeling et al, 2004), which showed that the sequence content and character (that is, G þ C content, codon usage) are nearly identical among the four NAG1 replicates, and that these assemblies differ significantly compared with four representative phyla within the domain Archaea, including those from the Crenarchaeota, Euryarchaeota and Thaumarchaeota (Figure 1b).…”

“…Previous studies of acidic ferric iron mats, in particular, have shown a remarkable diversity of archaea, which corresponds with the combination of unique geochemistry and high temperature of these systems (Inskeep et al, 2005;Kozubal et al, 2008;Inskeep et al, 2010;Kozubal et al, 2012). Prior 16S rRNA gene sequencing of high-temperature (65-80 1C) acidic Fe-oxide mats has revealed the presence of novel archaea, but cultivation of representative(s) from this group has yet to be successful.…”

Lrs14 transcriptional regulators influence biofilm formation and cell motility of Crenarchaea

“…Archaea form biofilms within many microbial ecosystems such as acid mine drainage sites, seafloor sediments or acidic hot springs mats (Baker and Banfield, 2003;Orcutt et al, 2011); Kozubal et al, 2012). Initial description of the archaeal biofilms were reported in the euryarchaeota Archaeoglobus fulgidus (Lapaglia and Hartzell, 1997) and in the bi-species biofilm of Pyrococcus furiosus and Methanopyrus kandlerii (Schopf et al, 2008).…”

Viral assemblage composition in Yellowstone acidic hot springs assessed by network analysis

“…High temperatures (480C), low pH (pHo3) conditions generally favor Archaea-dominated communities (Bolduc et al, 2012). Bacteria and eukaryotes are few or in many cases, absent (Reysenbach et al, 1994;Blank et al, 2002;Kozubal et al, 2012;Macur et al, 2012;Jay et al, 2013). These extreme environmental conditions favor not only the Archaea but also result in a relatively simplified microbial community structure.…”