Data from: Not so old Archaea - the antiquity of biogeochemical processes in the archaeal domain of life

Since the archaeal domain of life was first recognized, it has often been assumed that Archaea are ancient, and harbor primitive traits. In fact, the names of the major archaeal lineages reflect our assumptions regarding the antiquity of their traits. Ancestral state reconstruction and relaxed molecular clock analyses using newly articulated oxygen age constraints show that although the archaeal domain itself is old, tracing back to the Archean eon, many clades and traits within the domain are not ancient or primitive. Indeed many clades and traits, particularly in the Euryarchaeota, were inferred to be Neoproterozoic or Phanerozoic in age. Both Eury- and Crenarchaeota show increasing metabolic and physiological diversity through time. Early archaeal microbial communities were likely limited to sulfur reduction and hydrogenotrophic methanogenesis, and were confined to high-temperature geothermal environments. However, after the appearance of atmospheric oxygen, nodes containing a wide variety of traits (sulfate and thiosulfate reduction, sulfur oxidation, sulfide oxidation, aerobic respiration, nitrate reduction, mesophilic methanogenesis in sedimentary environments) appear, first in environments containing terrestrial Crenarchaeota in the Meso/Neoproterozoic followed by environments containing marine Euryarchaeota in the Neoproterozoic and Phanerozoic. This provides phylogenetic evidence for increasing complexity in the biogeochemical cycling of C, N, and S through geologic time, likely as a consequence of microbial evolution and the gradual oxygenation of various compartments within the biosphere. This work has implications not only for the large-scale evolution of microbial communities and biogeochemical processes, but also for the interpretation of microbial biosignatures in the ancient rock record.

自生命域中的古菌域（Archaea）首次被识别以来，学界长期默认古菌是一类古老且保留原始性状的类群。事实上，主要古菌演化支的命名便反映了我们对其性状古老性的固有假设。借助新近确立的氧年代约束开展祖先状态重建与宽松分子钟分析后，研究显示：尽管古菌域本身可追溯至太古宙（Archean eon），起源极为古老，但该域内的诸多演化支与性状并非古老或原始。具体而言，诸多演化支与性状——尤其是广古菌门（Euryarchaeota）内的类群——被推断其起源年代为新元古代（Neoproterozoic）或显生宙（Phanerozoic）。广古菌门与泉古菌门（Crenarchaeota）的代谢与生理多样性均随地质时间推移持续升高。早期古菌微生物群落大概率仅能进行硫还原与氢营养型产甲烷作用，且仅局限于高温地热环境中。然而，在大气氧出现之后，携带多种代谢性状（硫酸盐与硫代硫酸盐还原、硫氧化、硫化物氧化、有氧呼吸、硝酸盐还原、沉积环境中嗜温产甲烷作用）的系统发育节点相继出现：最早出现于中元古代-新元古代的陆地泉古菌栖息环境，随后在新元古代至显生宙的海洋广古菌栖息环境中出现。该研究为碳、氮、硫的生物地球化学循环随地质时间推移愈发复杂提供了系统发育学证据，这一过程大概率由微生物演化以及生物圈各圈层的逐步氧化作用共同促成。本研究不仅对微生物群落与生物地球化学过程的宏观演化具有重要启示，同时也为古老岩石记录中微生物生物标志物（biosignatures）的解译提供了参考依据。