Zepeda Mendoza Marie Lisandra, Lundberg Johannes, Ivarsson Magnus, Campos Paula, Nylander Johan A A, Sallstedt Therese, Dalen Love
Centre for GeoGenetics, University of Copenhagen, Natural History Museum of Denmark, Copenhagen, Denmark.
Department of Botany, Swedish Museum of Natural History, Stockholm, Sweden.
PLoS One. 2016 Mar 17;11(3):e0151577. doi: 10.1371/journal.pone.0151577. eCollection 2016.
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.
洞穴沉积物是次生矿物沉积物，通常由富含碳酸钙的水渗入地下洞穴形成，并且常与低营养和大多无光养的环境相关。Tjuv-Ante洞穴是一个由海浪作用形成的浅深度洞穴，主要成分是花岗岩和辉绿岩，欧泊-A和方解石是洞穴沉积物的一部分，使其成为一种罕见的洞穴类型。我们从Tjuv-Ante洞穴的一个洞穴沉积物内部生成了两个DNA鸟枪法测序宏基因组数据集，分别代表古老和相对较新的洞穴沉积物形成区域。我们使用这些数据集进行了以下操作：i）评估这些洞穴沉积物作为过去生物多样性档案库的用途；ii）对洞穴沉积物不同形成时期进行功能和分类学分析；iii）将宏基因组结果与同一洞穴附近另一个洞穴沉积物先前的显微镜分析结果进行分类学比较。我们的分析证实了放线菌和真菌的丰度，正如之前对该洞穴的显微镜分析所报告的那样，但我们也发现了更丰富的生物多样性。有趣的是，我们鉴定出了光合基因以及与铁和硫代谢相关的基因，这表明存在化学自养生物。此外，我们还鉴定出了与生物矿化相关的分类群和功能。然而，由于洞穴外部可能的淋溶以及我们认为是由真菌化学蚀刻导致的DNA损伤，我们无法确定地将这种类型的洞穴沉积物用作生物古档案库。
