Longitudinal analysis of the Five Sisters hot springs in Yellowstone National Park reveals a dynamic thermoalkaline environment

Abstract

Research focused on microbial populations of thermoalkaline springs has been driven in a large part by the lure of discovering functional enzymes with industrial applications in high-pH and high temperature environments. While several studies have focused on understanding the fundamental ecology of these springs, the small molecule profiles of thermoalkaline springs have largely been overlooked. To better understand how geochemistry, small molecule composition, and microbial communities are connected, we conducted a three-year study of the Five Sisters (FS) springs that included high-resolution geochemical measurements, 16S rRNA sequencing of the bacterial and archaeal community, and mass spectrometry-based metabolite and extracellular small molecule characterization. Integration of the four datasets facilitated a comprehensive analysis of the interwoven thermoalkaline spring system. Over the course of the study, the microbial population responded to changing environmental conditions, with archaeal populations decreasing in both relative abundance and diversity compared to bacterial populations. Decreases in the relative abundance of Archaea were associated with environmental changes that included decreased availability of specific nitrogen- and sulfur-containing extracellular small molecules and fluctuations in metabolic pathways associated with nitrogen cycling. This multi-factorial analysis demonstrates that the microbial community composition is more closely correlated with pools of extracellular small molecules than with the geochemistry of the thermal springs. This is a novel finding and suggests that a previously overlooked component of thermal springs may have a significant impact on microbial community composition.

Metagenomic analysis of hot spring soil for mining a novel thermostable enzybiotic

“…The classification of the representative thermophilic bacterial genera that were identified (Fig. 1 b) is in good agreement with similar studies on hot springs soil samples (Sharp et al 2014 ; Lavrentyeva et al 2018 ; Kochetkova et al 2020 ; Shu and Huang 2022 ; Peach et al 2022 ).…”

“…Ami1 was discovered through mining of soil metagenomic libraries collected from the hot springs of Lesvos Island. Soil from geothermal springs is a challenging natural environment which can give valuable genetic resources, regarding the microbial community size and the diversity of species present including thermophilic and hyperthermophilic microorganisms (Sharp et al 2014 ; Lavrentyeva et al 2018 ; Kochetkova et al 2020 ; Shu and Huang 2022 ; Peach et al 2022 ). Omics technologies such as a marker gene analysis which includes the 16S rRNA gene have revolutionized our insight of microbial diversity and ecology, allowing a better understanding of the microbial communities and their relationships across different taxa, phylogenies, and functional composition in space and time (Goh et al 2022 ; Shaffer et al 2022 ).…”

Assessing microbial diversity in Yellowstone National Park hot springs using a field deployable automated nucleic acid extraction system

“…In such an extreme environment, dominant microbes of certain microbial populations were documented based on targeted gene amplification/sequencing (Barns et al, 1994;Blank et al, 2002;Podar et al, 2020) and shotgun metagenome sequencing methods (Colman et al, 2022). Though previous metagenomic studies have been conducted at OS (Klatt et al, 2011), to date only 16S rRNA gene targeted amplicon sequencing has been used to discern the microbial community composition in the FSS hot spring system (Peach et al, 2022). To our knowledge, work here is the first to generate shotgun metagenomics sequencing from the FSS system hot spring complex.…”

Field deployable automated nucleic acid extraction system enables rapid on-site measurement of microbial diversity of Yellowstone National Park hot springs

“…In such an extreme environment, dominant microbes of certain microbial populations were documented based on targeted gene amplification/sequencing [17][18][19] and shotgun metagenome sequencing methods [20]. Though previous metagenomic studies have been conducted at Octopus hot spring [3], to date only 16S rRNA gene targeted amplicon sequencing has been used to discern the microbial community composition in the FSS hot spring system [21]. To our knowledge, work here is the first to generate shotgun metagenomics sequencing from the FSS system hot spring complex.…”