Metagenomic Analysis from the Interior of a Speleothem in Tjuv-Ante's Cave, Northern Sweden

Speleothems are secondary mineral deposits normally formed by water supersaturated with calcium carbonate percolating into underground caves, and are often associated with low-nutrient and mostly non-phototrophic conditions. Tjuv-Ante’s cave is a shallow-depth cave formed by the action of waves, with granite and dolerite as major components, and opal-A and calcite as part of the speleothems, making it a rare kind of cave. We generated two DNA shotgun sequencing metagenomic datasets from the interior of a speleothem from Tjuv-Ante’s cave representing areas of old and relatively recent speleothem formation. We used these datasets to perform i) an evaluation of the use of these speleothems as past biodiversity archives, ii) functional and taxonomic profiling of the speleothem’s different formation periods, and iii) taxonomic comparison of the metagenomic results to previous microscopic analyses from a nearby speleothem of the same cave. Our analyses confirm the abundance of Actinobacteria and fungi as previously reported by microscopic analyses on this cave, however we also discovered a larger biodiversity. Interestingly, we identified photosynthetic genes, as well as genes related to iron and sulphur metabolism, suggesting the presence of chemoautotrophs. Furthermore, we identified taxa and functions related to biomineralization. However, we could not confidently establish the use of this type of speleothems as biological paleoarchives due to the potential leaching from the outside of the cave and the DNA damage that we propose has been caused by the fungal chemical etching.

洞穴次生沉积物（speleothems）是碳酸钙过饱和水溶液渗入地下洞穴后形成的次生矿物沉积，通常形成于低营养且几乎不依赖光合作用的环境中。提乌夫-安特洞穴（Tjuv-Ante’s Cave）是一处由海浪作用塑造的浅埋洞穴，主要矿物组成为花岗岩与辉绿岩，其洞穴沉积物包含A型蛋白石（opal-A）与方解石，属于罕见的洞穴类型。本研究从该洞穴的一处洞穴沉积物内部获取了两套鸟枪法宏基因组测序数据集（DNA shotgun sequencing metagenomic datasets），分别对应该沉积物的古老沉积阶段与相对较新的沉积阶段。基于上述数据集，我们开展了三项研究：i）评估此类洞穴沉积物作为古生物多样性档案的应用潜力；ii）对不同沉积时期的洞穴沉积物进行功能与分类学谱分析；iii）将宏基因组分析结果与该洞穴内邻近另一处洞穴沉积物的既往显微分析结果进行分类学对比。我们的分析证实了放线菌门（Actinobacteria）与真菌的高丰度，与此前该洞穴的显微分析结果一致，但同时也发现了更为丰富的生物多样性。值得注意的是，我们鉴定出了光合相关基因，以及与铁、硫代谢相关的基因，提示存在化能自养微生物（chemoautotrophs）。此外，我们还识别出与生物矿化作用相关的类群与功能通路。然而，由于洞穴外部物质的潜在淋溶作用，以及我们推测由真菌化学侵蚀导致的DNA损伤，我们尚无法确认此类洞穴沉积物可作为可靠的古生物档案。