Data from: Metabolic characteristics of dominant microbes and key rare species from an acidic hot spring in Taiwan revealed by metagenomics

Background: Microbial 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. Results: In 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. Conclusions: Our 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.

背景：酸性热泉中的微生物多样性与群落结构，此前多通过基于16S rRNA基因的多样性测序进行解析。但目前学界对微生物间互作，以及微生物与环境因子间的互作关系仍缺乏深入认知。
结果：本研究采用宏基因组学方法结合后续生物信息学分析，对中国台湾北部酸性热泉石坪（Shi-Huang-Ping，简称SHP）内的微生物生态系统互作关系进行预测。通过对环境参数与潜在代谢通路的解析，明确了碳同化途径的核心重要性。研究在5个优势细菌属中鉴定出4种截然不同的碳同化途径。在这些优势固碳微生物中，氢杆菌属（Hydrogenobaculum）细菌相较于其他碳同化微生物具有竞争优势，成为SHP中的优势类群，推测与其可代谢氢气、耐受温度波动的厌氧环境的能力相关。此外，多数优势微生物均能够代谢在SHP中含量丰富的无机硫类化合物。但在关键稀有微生物类群中，唯有氧化亚铁硫杆菌（Acidithiobacillus ferrooxidans）具备固氮能力，提示其在氮循环中发挥关键作用。除潜在代谢互作外，本研究基于纳米古菌（Nanoarchaeum）相关序列、其潜在宿主炽热球菌属（Ignicoccus）相关古菌序列，以及病毒序列与CRISPR阵列（CRISPR arrays），推断该生态系统中存在复杂的微生物间互作关系。
结论：本研究证实，酸性热泉中的微生物群落内部存在大量微生物间及微生物与环境间的互作关系。本研究提出，氢杆菌属（Hydrogenobaculum）细菌可通过代谢氢气、同化碳源并耐受温度波动的厌氧环境，成为该酸性热泉中的优势微生物类群。