Table_1_Whither the genus Caldicellulosiruptor and the order Thermoanaerobacterales: phylogeny, taxonomy, ecology, and phenotype.XLSX

The order Thermoanaerobacterales currently consists of fermentative anaerobic bacteria, including the genus Caldicellulosiruptor. Caldicellulosiruptor are represented by thirteen species; all, but one, have closed genome sequences. Interest in these extreme thermophiles has been motivated not only by their high optimal growth temperatures (≥70°C), but also by their ability to hydrolyze polysaccharides including, for some species, both xylan and microcrystalline cellulose. Caldicellulosiruptor species have been isolated from geographically diverse thermal terrestrial environments located in New Zealand, China, Russia, Iceland and North America. Evidence of their presence in other terrestrial locations is apparent from metagenomic signatures, including volcanic ash in permafrost. Here, phylogeny and taxonomy of the genus Caldicellulosiruptor was re-examined in light of new genome sequences. Based on genome analysis of 15 strains, a new order, Caldicellulosiruptorales, is proposed containing the family Caldicellulosiruptoraceae, consisting of two genera, Caldicellulosiruptor and Anaerocellum. Furthermore, the order Thermoanaerobacterales also was re-assessed, using 91 genome-sequenced strains, and should now include the family Thermoanaerobacteraceae containing the genera Thermoanaerobacter, Thermoanaerobacterium, Caldanaerobacter, the family Caldanaerobiaceae containing the genus Caldanaerobius, and the family Calorimonaceae containing the genus Calorimonas. A main outcome of ANI/AAI analysis indicates the need to reclassify several previously designated species in the Thermoanaerobacterales and Caldicellulosiruptorales by condensing them into strains of single species. Comparative genomics of carbohydrate-active enzyme inventories suggested differentiating phenotypic features, even among strains of the same species, reflecting available nutrients and ecological roles in their native biotopes.

热厌氧杆菌目（Thermoanaerobacterales）目前包含发酵型厌氧菌，其中涵盖解纤维素菌属（Caldicellulosiruptor）。该属目前共有13个物种，除1个物种外，其余均已获得闭合基因组序列。这类极端嗜热菌受到学界关注的原因，不仅在于其最优生长温度高达70℃及以上，还在于其具备水解多糖类物质的能力——对于部分物种而言，可同时降解木聚糖与微晶纤维素。解纤维素菌属的菌株已从新西兰、中国、俄罗斯、冰岛及北美等全球不同地理区域的热液陆地生境中分离得到；而在其他陆地生境中，其存在的证据则来自宏基因组特征，例如永久冻土中的火山灰样本。本研究基于新获得的基因组序列，重新审视了解纤维素菌属的系统发育与分类学地位。通过对15株菌株的基因组分析，本研究提议建立一个新的目——解纤维素菌目（Caldicellulosiruptorales），该目下设解纤维素菌科（Caldicellulosiruptoraceae），包含解纤维素菌属（Caldicellulosiruptor）与厌氧纤维菌属（Anaerocellum）两个属。此外，本研究还利用91株已完成基因组测序的菌株，对热厌氧杆菌目（Thermoanaerobacterales）进行了重新评估，修正后的该目应包含如下类群：热厌氧杆菌科（Thermoanaerobacteraceae），包含热厌氧杆菌属（Thermoanaerobacter）、热厌氧囊菌属（Thermoanaerobacterium）、Cald厌氧杆菌属（Caldanaerobacter）；Cald厌氧杆菌科（Caldanaerobiaceae），仅包含Cald厌氧杆菌属（Caldanaerobius）；以及产热单胞菌科（Calorimonaceae），仅包含产热单胞菌属（Calorimonas）。平均核苷酸同源性（Average Nucleotide Identity, ANI）/平均氨基酸同源性（Average Amino Acid Identity, AAI）分析的核心结果显示，需对热厌氧杆菌目与解纤维素菌目中的多个已命名物种进行重新分类，将其归并为单一物种的菌株。对碳水化合物活性酶编码基因库的比较基因组学分析显示，即使是同一物种的不同菌株，其表型特征也存在差异，这反映了它们在原生生境中可利用的营养物质与生态位功能。