Microbiology Meets Archaeology: Soil Microbial Communities Reveal Different Human Activities at Archaic Monte Iato (Sixth Century BC)

Abstract

Microbial ecology has been recognized as useful in archaeological studies. At Archaic Monte Iato in Western Sicily, a native (indigenous) building was discovered. The objective of this study was the first examination of soil microbial communities related to this building. Soil samples were collected from archaeological layers at a ritual deposit (food waste disposal) in the main room and above the fireplace in the annex. Microbial soil characterization included abundance (cellular phospholipid fatty acids (PLFA), viable bacterial counts), activity (physiological profiles, enzyme activities of viable bacteria), diversity, and community structure (bacterial and fungal Illumina amplicon sequencing, identification of viable bacteria). PLFA-derived microbial abundance was lower in soils from the fireplace than in soils from the deposit; the opposite was observed with culturable bacteria. Microbial communities in soils from the fireplace had a higher ability to metabolize carboxylic and acetic acids, while those in soils from the deposit metabolized preferentially carbohydrates. The lower deposit layer was characterized by higher total microbial and bacterial abundance and bacterial richness and by a different carbohydrate metabolization profile compared to the upper deposit layer. Microbial community structures in the fireplace were similar and could be distinguished from those in the two deposit layers, which had different microbial communities. Our data confirmed our hypothesis that human consumption habits left traces on microbiota in the archaeological evidence; therefore, microbiological residues as part of the so-called ecofacts are, like artifacts, key indicators of consumer behavior in the past.Electronic supplementary materialThe online version of this article (doi:10.1007/s00248-016-0904-8) contains supplementary material, which is available to authorized users.

Characterization of soil bacterial, archaeal and fungal communities inhabiting archaeological human-impacted layers at Monte Iato settlement (Sicily, Italy)

“…The coming together of archaeology and microbiology promises to revolutionize the analysis and interpretation of archaeological deposits 1 . In this way, the few existing works studying the microbial communities associated with archaeological samples such as dental calculi 2 , bones 3 , different kinds of organic remains 4 , anthropogenically-impacted soils 5 – 8 and mud 6 , 9 have confirmed the efficacy of this new direction of analysis in archaeology that may impact on the formulation of theories and our understanding of past events 1 .…”

“…Former studies have already used microbial communities as bioindicators, termed as ecofacts by Margesin, et al . 5 , of human activities in the past. Soil fungal communities inhabiting anthropogenically transformed layers of medieval Russian settlements differed from those associated with non-impacted surrounding soils 13 .…”

Releasing the microbes from old bones: the effect of different DNA extraction protocols on microbial community profiling

“…However given that the majority (>50%) of this diverse community could not successfully be classified, and was significantly different from the taxa found using the other methods, it seems that most of this community comprises of taxa that are rare. Although there is a higher overall diversity and consistency in the PCR triplicates using the raw method, the dominating bacterial phyla ( Figure S1a) found have previously been associated with environmental contaminants such as soil (Margesin et al 2017;Zaremba-Niedzwiedzka and Andersson 2013). Furthermore, given that quantitative real-time PCR analysis of the extracts indicated that the "raw" extracts contained up to 1000-fold less bacterial DNA than in the extracts from the three EDTA based methods (data not shown), we speculate that their signal is subsequently lost among the flood of more common microbial taxa recovered when fully digesting the bone with EDTA, hence why their overall diversity appears lower.…”

“…Metcalf et al (2013) also found Firmicutes dominated the initial bacterial community associated with degrading mouse cadavers, however the study focussed on soft tissue decomposition and not bone material. Actinobacteria are also known to be present in sediments where they play a crucial role in the degradation of biomaterials (Goodfellow and Williams 1983;Margesin et al 2017). That we find these phyla in our bone sample is therefore not surprising.…”

Hadesarchaea and other extremophile bacteria from ancient mining areas of the East Harz region (Germany) suggest an ecological long-term memory of soil

“…Probably, even storage of bacteria over huge time scales is possible as investigations on inclusions in Permian salt deposits suggest [28]. Despite geological memory effects, even special historic or prehistoric situations can cause special local components in microbial communities which are related to ancient human activities [15,21].…”