Extremophiles in Soil Communities of Former Copper Mining Sites of the East Harz Region (Germany) Reflected by Re-Analyzed 16S rRNA Data

Abstract

The east and southeast rim of Harz mountains (Germany) are marked by a high density of former copper mining places dating back from the late 20th century to the middle age. A set of 18 soil samples from pre- and early industrial mining places and one sample from an industrial mine dump have been selected for investigation by 16S rRNA and compared with six samples from non-mining areas. Although most of the soil samples from the old mines show pH values around 7, RNA profiling reflects many operational taxonomical units (OTUs) belonging to acidophilic genera. For some of these OTUs, similarities were found with their abundances in the comparative samples, while others show significant differences. In addition to pH-dependent bacteria, thermophilic, psychrophilic, and halophilic types were observed. Among these OTUs, several DNA sequences are related to bacteria which are reported to show the ability to metabolize special substrates. Some OTUs absent in comparative samples from limestone substrates, among them Thaumarchaeota were present in the soil group from ancient mines with pH > 7. In contrast, acidophilic types have been found in a sample from a copper slag deposit, e.g., the polymer degrading bacterium Granulicella and Acidicaldus, which is thermophilic, too. Soil samples of the group of pre-industrial mines supplied some less abundant, interesting OTUs as the polymer-degrading Povalibacter and the halophilic Lewinella and Halobacteriovorax. A particularly high number of bacteria (OTUs) which had not been detected in other samples were found at an industrial copper mine dump, among them many halophilic and psychrophilic types. In summary, the results show that soil samples from the ancient copper mining places contain soil bacterial communities that could be a promising source in the search for microorganisms with valuable metabolic capabilities.

Archaeal and Extremophilic Bacteria from Different Archaeological Excavation Sites

“…In the soils of the burial sites of Jingzhou, China (about 5th to 3rd century BC), Crenarchaeota have been identified, but in a low content next to the more than 95% of Proteobacteria , Actinobacteria , Bacteriodetes and Firmicutes ([ 44 ], Figure 1). Archaea had been found up to a content of about 8% in some soil samples from the ancient copper mining areas of the East Harz region [ 45 ]. NGS investigations on soil bacteria communities of historical rice fields speak to the fact that methanogenic Archaea could be used as an indicator for medieval rice cultivation [ 46 ].…”

Application of the Next Generation Sequencing in Biology and Medicine

“…Soil samples can be also analyzed by the NGS to assess the microbial diversity and the presence of various organisms, including fungi, bacteria, and small invertebrates. NGS can be also applied to air samples to capture genetic material from airborne organisms, such as pollen, spores, and microorganisms (Köhler, 2021).…”