Three Soil Bacterial Communities from an Archaeological Excavation Site of an Ancient Coal Mine near Bennstedt (Germany) Characterized by 16S r-RNA Sequencing

Abstract

This metagenomics investigation of three closely adjacent sampling sites from an archaeological excavation of a pre-industrial coal mining exploration shaft provides detailed information on the composition of the local soil bacterial communities. The observed significant differences between the samples, reflected in the 16S r-RNA analyses, were consistent with the archaeologically observed situation distinguishing the coal seam, the rapidly deposited bright sediment inside an exploration shaft, and the topsoil sediment. In general, the soils were characterized by a dominance of Proteobacteria, Actinobacteria, Acidobacteria, and Archaea, whereas the coal seam was characterized by the highest proportion of Proteobacteria; the topsoil was characterized by very high proportions of Archaea—in particular, Nitrosotaleaceae—and Acidobacteria, mainly of Subgroup 2. Interestingly, the samples of the fast-deposited bright sediment showed a rank function of OTU abundances with disproportional values in the lower abundance range. This could be interpreted as a reflection of the rapid redeposition of soil material during the refilling of the exploration shaft in the composition of the soil bacterial community. This interpretation is supported by the observation of a comparatively high proportion of reads relating to bacteria known to be alkaliphilic in this soil material. In summary, these investigations confirm that metagenomic analyses of soil material from archaeological excavations can provide valuable information about the local soil bacterial communities and the historical human impacts on them.

Archaeal and Extremophilic Bacteria from Different Archaeological Excavation Sites

“…The appearance of Micrarchaeota in the samples from the ancient coal mine area near Bennstedt corresponds to the fact that this archaeal phylum is related to acidic environments and can be associated with Thermoplasmatales [ 22 ]. Indeed, the three samples of Bennstedt showed the lowest pH values of the investigated soil samples (pH between 4.05 and 4.22 [ 23 ]).…”

Low Abundant Bacteria Reflect Soil Specificity—Analysis of Bacterial Communities from Archaeological Investigation of Pre-Industrial Saline Ash Deposits of Bad Dürrenberg (Germany)

“…For comparison, also some NGS-data from a sample set of Bennstedt were used, here [12]. These samples had been taken from an ancient coal mine prospection shaft.…”

“…For a short explanation, a scheme of sample and data processing steps is shown in Figure S2. The details of the whole process of sample preparation, DNA analysis, data processing and taxonomical analysis were performed as described previously [12]. The SILVA database was used for identification of bacteria from the sequence data [21][22][23].…”

“…A similar strong shoulder was observed in the rank diagram of samples from the translocated bright sediment found inside the shaft hole of the pre-industrial coal prospection near Bennstedt (samples HB58-1 and HB58-2). There was already proposed to interpret such a shoulder as a disturbance of smooth numerical distribution of abundances in soil bacterial communities which might be due to the previous transfer of soil material from one environment to another [12]. Conversely, such an interpretation would suggest that the presence of moderate to lower abundant OTUs, or their DNA, retains information about the ecological history of a location.…”

“…These ancient impacts must not only be considered as early damage to the soil but should also be recognized as contributions to the Beta diversity of soil bacterial communities of a certain area. Variation in the soil bacterial compositions of closely adjacent sampling sites indicates that human activities over many centuries or even millennia have had an impact on the recent state of the soil [10][11][12]. Due to the smaller scale of land use patterns in most prehistoric, medieval or early modern-period activities, many different soil conditions and microbial communities can be expected in a comparatively small area.…”