Abstract
BackgroundMicrobial diversity and community structures in acidic hot springs have been characterized by 16S rRNA gene-based diversity surveys. However, our understanding regarding the interactions among microbes, or between microbes and environmental factors, remains limited.ResultsIn the present study, a metagenomic approach, followed by bioinformatics analyses, were used to predict interactions within the microbial ecosystem in Shi-Huang-Ping (SHP), an acidic hot spring in northern Taiwan. Characterizing environmental parameters and potential metabolic pathways highlighted the importance of carbon assimilatory pathways. Four distinct carbon assimilatory pathways were identified in five dominant genera of bacteria. Of those dominant carbon fixers, Hydrogenobaculum bacteria outcompeted other carbon assimilators and dominated the SHP, presumably due to their ability to metabolize hydrogen and to withstand an anaerobic environment with fluctuating temperatures. Furthermore, most dominant microbes were capable of metabolizing inorganic sulfur-related compounds (abundant in SHP). However, Acidithiobacillus ferrooxidans was the only species among key rare microbes with the capability to fix nitrogen, suggesting a key role in nitrogen cycling. In addition to potential metabolic interactions, based on the 16S rRNAs gene sequence of Nanoarchaeum-related and its potential host Ignicoccus-related archaea, as well as sequences of viruses and CRISPR arrays, we inferred that there were complex microbe-microbe interactions.ConclusionsOur study provided evidence that there were numerous microbe-microbe and microbe-environment interactions within the microbial community in an acidic hot spring. We proposed that Hydrogenobaculum bacteria were the dominant microbial genus, as they were able to metabolize hydrogen, assimilate carbon and live in an anaerobic environment with fluctuating temperatures.Electronic supplementary materialThe online version of this article (doi:10.1186/s12864-015-2230-9) contains supplementary material, which is available to authorized users.
Highlights
Microbial diversity and community structures in acidic hot springs have been characterized by 16S rRNA gene-based diversity surveys
Microbial diversity surveys based on 16S rRNA gene are the most common culture-independent method to characterize composition of a microbial community and to compare microbial diversity among habitats [1]
Diverse microenvironments in SHP implied by microbial composition To further elucidate interactions between microbes and environmental factors in SHP, we critically reviewed previous reports of dominant microbes in SHP
Summary
Microbial diversity and community structures in acidic hot springs have been characterized by 16S rRNA gene-based diversity surveys. Microbial diversity surveys based on 16S rRNA gene are the most common culture-independent method to characterize composition of a microbial community and to compare microbial diversity among habitats [1]. Characterizing composition of microbial communities could provide insights regarding potential metabolic interactions among microbes or between microbes and environmental factors, additional methods are required for more comprehensive understanding. A metagenomic approach could be used to characterize potential metabolic activities of microbial communities. In a comparative metagenomic study, Inskeep et al characterized diverse metabolic strategies related to geochemical characteristics of two acidic hot springs (Crater Hills and Norris Geysers Basin) in Yellowstone National Park [18]. In contrast to the El Coquito spring, microbes in Crater Hills and Norris Geysers Basin adopted non-photosynthetic carbon assimilation pathways (reductive citrate cycle), apparently because water temperatures of these springs (>65 °C) approached upper temperature limits for photosynthesis [19]
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