Characterization of soil bacterial, archaeal and fungal communities inhabiting archaeological human-impacted layers at Monte Iato settlement (Sicily, Italy)
Language English Country England, Great Britain Media electronic
Document type Journal Article, Research Support, Non-U.S. Gov't
PubMed
29382933
PubMed Central
PMC5789874
DOI
10.1038/s41598-018-20347-8
PII: 10.1038/s41598-018-20347-8
Knihovny.cz E-resources
- MeSH
- Archaea genetics MeSH
- Archaeology methods MeSH
- Bacteria genetics MeSH
- Biodiversity MeSH
- DNA, Bacterial genetics MeSH
- DNA, Fungal genetics MeSH
- Nitrogen metabolism MeSH
- Ecosystem MeSH
- Fungi genetics MeSH
- Humans MeSH
- Human Activities MeSH
- Soil MeSH
- Soil Microbiology MeSH
- Carbon metabolism MeSH
- Check Tag
- Humans MeSH
- Publication type
- Journal Article MeSH
- Research Support, Non-U.S. Gov't MeSH
- Geographicals
- Sicily MeSH
- Names of Substances
- DNA, Bacterial MeSH
- DNA, Fungal MeSH
- Nitrogen MeSH
- Soil MeSH
- Carbon MeSH
Microbial communities in human-impacted soils of ancient settlements have been proposed to be used as ecofacts (bioindicators) of different ancient anthropogenic activities. In this study, bacterial, archaeal and fungal communities inhabiting soil of three archaic layers, excavated at the archaeological site on Monte Iato (Sicily, Italy) and believed to have been created in a chronological order in archaic times in the context of periodic cultic feasts, were investigated in terms of (i) abundance (phospholipid fatty acid (PLFA) analysis and quantitative PCR)), (ii) carbon(C)-source consumption patterns (Biolog-Ecoplates) and (iii) diversity and community composition (Illumina amplicon sequencing). PLFA analyses demonstrated the existence of living bacteria and fungi in the soil samples of all three layers. The upper layer showed increased levels of organic C, which were not concomitant with an increment in the microbial abundance. In taxonomic terms, the results indicated that bacterial, archaeal and fungal communities were highly diverse, although differences in richness or diversity among the three layers were not detected for any of the communities. However, significantly different microbial C-source utilization patterns and structures of bacterial, archaeal and fungal communities in the three layers confirmed that changing features of soil microbial communities reflect different past human activities.
Institute of Archaeologies University of Innsbruck Langer Weg 11 A 6020 Innsbruck Austria
Institute of Microbiology University of Innsbruck Technikerstrasse 25 A 6020 Innsbruck Austria
See more in PubMed
Garg, P. & Shukla, P. Archaeology vis-à-vis microbiology: Discoreving the vistas of interdisciplinary research in Frontier Discoveries and Innovations in Interdisciplinary Microbiology (ed. Shukla, P.) 213–219 (Springer India, 2016).
Santiago-Rodriguez TM, Narganes-Storde Y, Chanlatte-Baik L, Toranzos GA, Cano RJ. Insights of the dental calculi microbiome of pre-Columbian inhabitants from Puerto Rico. PeerJ. 2017;5:e3277. doi: 10.7717/peerj.3277. PubMed DOI PMC
Antoine S, Child A, Nicholson R, Pollard A. The biochemistry and microbiology of buried human bone, in relation to dietary reconstruction. Circaea. 1992;9:65–79.
Douterelo I, Goulder R, Lillie M. Response of the microbial community to water table variation and nutrient addition and its implications for in situ preservation of organic archaeological remains in wetland soils. Int. Biodeter. Biodegr. 2009;63:795–805. doi: 10.1016/j.ibiod.2009.06.010. DOI
Margesin R, Siles JA, Cajthaml T, Öhlinger B, Kistler E. Microbiology meets archaeology: Soil microbial communities reveal different human activities at archaic Monte Iato (sixth century BC) Microb. Ecol. 2017;73:925–938. doi: 10.1007/s00248-016-0904-8. PubMed DOI PMC
Xu J, Wei Y, Jia H, Xiao L, Gong D. A new perspective on studying burial environment before archaeological excavation: Analyzing bacterial community distribution by high-throughput sequencing. Sci. Rep. 2017;7:41691. doi: 10.1038/srep41691. PubMed DOI PMC
Demkina TS, Khomutova TE, Kashirskaya NN, Stretovich IV, Demkin VA. Microbiological investigations of paleosols of archeological monuments in the steppe zone. Eurasian Soil Sci. 2010;43:194–201. doi: 10.1134/S1064229310020092. DOI
Ivanova AE, Marfenina OE, Kislova EE, Zazovskaya EP. Mycological characteristics of the cultural layer of a medieval settlement on soddy calcareous soils. Eurasian Soil Sci. 2006;39:53–61. doi: 10.1134/S1064229306010078. DOI
Mulec J, et al. Microbiology of healing mud (fango) from Roman thermae aquae iasae archaeological site (Varaždinske Toplice, Croatia) Microb. Ecol. 2015;69:293–306. doi: 10.1007/s00248-014-0491-5. PubMed DOI
Ivanova A, Marfenina O. Soil fungal communities as bioindicators of ancient human impacts in medieval settlements in different geographic regions of Russia and southwestern Kazakhstan. Quatern. Int. 2015;365:212–222. doi: 10.1016/j.quaint.2014.10.016. DOI
Peters S, Borisov AV, Reinhold S, Korobov DS, Thiemeyer H. Microbial characteristics of soils depending on the human impact on archaeological sites in the Northern Caucasus. Quatern. Int. 2014;324:162–171. doi: 10.1016/j.quaint.2013.11.020. DOI
Khomutova TE, Demkina TS, Demkin VA. The state of microbial communities in buried paleosols in relation to prevailing climates in steppes of the Lower Volga region. Quatern. Int. 2014;324:115–123. doi: 10.1016/j.quaint.2014.01.039. DOI
Marfenina OE, Gorbatovskaya EV, Gorlenko MV. Mycological characterization of the occupation deposits in excavated medieval Russian settlements. Microbiology. 2001;70:738–742. doi: 10.1023/A:1013152202535. PubMed DOI
Kistler, E. Wohnen in Compounds: Haus-Gesellschaften und soziale Gruppenbildung im Frühen West- und Mittelsizilien (12-6 Jh. v. Chr.) In Communicating identity in Italic Iron Age communities (eds Gleba, M. & Horsnaes, H.W.) 130–154 (Oxbow Books, 2011).
Öhlinger, B. Ritual und Religion im archaischen Sizilien. Formations- und Transformationsprozesse binnenländischer Kultorte im Kontext kultureller Kontakte, Italikà 4 (Ludwig Reichert Verlag, 2015).
Öhlinger, B. Indigenous cult places of local and interregional scale in archaic Sicily: A sociological approach to religion in Sanctuaries and the power of consumption. Networking and the formation of elites in the archaic Western Mediterranean world (eds Kistler, E., Öhlinger, B., Mohr, M. & Hoernes, M.) 417–430 (Harrassowitz Verlag, 2015).
Isler HP. Grabungen auf dem Monte Iato. Antike Kunst. 2008;51:134–145.
Kistler E, Öhlinger B, Mölk N, Steger M. Zwischen Aphrodite-Tempel und spätarchaischem Haus. Die Innsbrucker Kampagnen 2012 und 2013 auf dem Monte Iato (Sizilien) Jahreshefte des Österreichischen Archäologischen Institutes in Wien. 2014;83:157–200.
Kistler E, et al. Zwischen Aphrodite-Tempel und spätarchaischem Haus II. Die Innsbrucker Kampagne 2014 auf dem Monte Iato (Sizilien) Jahreshefte des Österreichischen Archäologischen Institutes in Wien. 2015;84:129–164.
Kistler, E., Öhlinger, B., Th., D., Irovec, R. & Wimmer, B. Archaika as a resource: The Production of locality and colonial empowerment on Monte Iato (Western Sicily) around 500 BC in ResourceCultures: Sociocultural dynamics and the use of resources – Theories, methods and perspectives (eds Scholz, A. K., Bartelheim. M., Hardenberg, R. & Staecker, J.) 11–27 (Eberhard Karls Universität, (2017).
Kistler, E. & Öhlinger, B. Ergebnisse der fünften Grabungskampagne am Monte Iato der Universität Innsbruckhttps://www.uibk.ac.at/projects/monte-iato/working-papers/downloads/ergebnisse_2015_deutsch.pdf (2015).
Vassallo, S. & Valentino, M. Scavi nella necropoli occidentale di Himera, il paesaggio e le tipologie funerarie in Sicilia occidentale: Studi, rassegne, ricerche. Atti delle Settime Giornate internazionali di studi sull’area elima e la Sicilia occidentale nel contesto mediterraneo (Erice, 12–15 ottobre2009), a curadi C. Ampolo (ed. Ampolo C.)49–71 (Edizioni della Normale, 2012).
Blagodatskaya E, Kuzyakov Y. Active microorganisms in soil: Critical review of estimation criteria and approaches. Soil Biol. Biochem. 2013;67:192–211. doi: 10.1016/j.soilbio.2013.08.024. DOI
Janssen PH. Identifying the dominant soil bacterial taxa in libraries of 16S rRNA and 16S rRNA genes. Appl. Environ. Microb. 2006;72:1719–1728. doi: 10.1128/AEM.72.3.1719-1728.2006. PubMed DOI PMC
Youssef NH, Elshahed MS. Diversity rankings among bacterial lineages in soil. ISME J. 2009;3:305–313. doi: 10.1038/ismej.2008.106. PubMed DOI
Sørensen, J. & Nybroe, O. Pseudomonas in the soil environment in Pseudomonas: Volume 1 Genomics, Life Style and Molecular Architecture (ed. Ramos, J.L.) 369–401 (Springer US, (2004).
Nikel PI, Martinez-Garcia E, de Lorenzo V. Biotechnological domestication of pseudomonads using synthetic biology. Nat Rev Micro. 2014;12:368–379. doi: 10.1038/nrmicro3253. PubMed DOI
Tripathi BM, et al. Soil pH and biome are both key determinants of soil archaeal community structure. Soil Biol. Biochem. 2015;88:1–8. doi: 10.1016/j.soilbio.2015.05.004. DOI
Spang A, et al. The genome of the ammonia‐oxidizing Candidatus Nitrososphaera gargensis: Insights into metabolic versatility and environmental adaptations. Environ. Microbiol. 2012;14:3122–3145. doi: 10.1111/j.1462-2920.2012.02893.x. PubMed DOI
Tedersoo L, et al. Global diversity and geography of soil fungi. Science. 2014;346:1256688. doi: 10.1126/science.1256688. PubMed DOI
Benitez M-S, Taheri WI, Lehman RM. Selection of fungi by candidate cover crops. Appl. Soil Ecol. 2016;103:72–82. doi: 10.1016/j.apsoil.2016.03.016. DOI
Cabral A, Groenewald JZ, Rego C, Oliveira H, Crous PW. Cylindrocarpon root rot: Multi-gene analysis reveals novel species within the Ilyonectria radicicola species complex. Mycol. Prog. 2012;11:655–688. doi: 10.1007/s11557-011-0777-7. DOI
Siles, J. A., Cajthaml, T., Minerbi, S. & Margesin, R. Effect of altitude and season on microbial activity, abundance and community structure in Alpine forest soils. FEMS Microbiol. Ecol. 92, 10.1093/femsec/fiw008 (2016). PubMed
Šnajdr J, et al. Spatial variability of enzyme activities and microbial biomass in the upper layers of Quercus petraea forest soil. Soil Biol. Biochem. 2008;40:2068–2075. doi: 10.1016/j.soilbio.2008.01.015. DOI
Bligh EG, Dyer WJ. A rapid method of total lipid extraction and purification. Can. J. Biochem. Phys. 1959;37:911–917. doi: 10.1139/y59-099. PubMed DOI
Tornberg K, Bååth E, Olsson S. Fungal growth and effects of different wood decomposing fungi on the indigenous bacterial community of polluted and unpolluted soils. Biol. Fert. Soils. 2003;37:190–197.
Fierer N, Jackson JA, Vilgalys R, Jackson RB. Assessment of soil microbial community structure by use of taxon-specific quantitative PCR assays. Appl. Environ. Microb. 2005;71:4117–4120. doi: 10.1128/AEM.71.7.4117-4120.2005. PubMed DOI PMC
Cadillo-Quiroz H, et al. Vertical profiles of methanogenesis and methanogens in two contrasting acidic peatlands in central New York State, USA. Environ. Microbiol. 2006;8:1428–1440. doi: 10.1111/j.1462-2920.2006.01036.x. PubMed DOI
Chemidlin Prevost-Boure N, et al. Validation and application of a PCR primer set to quantify fungal communities in the soil environment by real-time quantitative PCR. PloS One. 2011;6:e24166. doi: 10.1371/journal.pone.0024166. PubMed DOI PMC
Castro HF, Classen AT, Austin EE, Crawford KM, Schadt CW. Development and validation of a citrate synthase directed quantitative PCR marker for soil bacterial communities. Appl. Soil Ecol. 2012;61:69–75. doi: 10.1016/j.apsoil.2012.05.007. DOI
Siles JA, Margesin R. Abundance and diversity of bacterial, archaeal, and fungal communities along an altitudinal gradient in Alpine forest soils: What are the driving factors? Microb. Ecol. 2016;72:207–220. doi: 10.1007/s00248-016-0748-2. PubMed DOI PMC
Lane, D. 16S/23S rRNA sequencing in Nucleic acid techniques in bacterial systematics (ed. E. Stackebrandt, E. & Goodfellow, M.) 125–175 (John Wiley & Sons, 1991).
White, T. J., Bruns, T., Lee, S. & Taylor, J. Amplification and direct sequencing of fungal ribosomal RNA genes for phylogenetics in PCR protocols: A guide to methods and applications (ed. Innis, M.A., Gelfand, D.H., Sninsky, J.J. & White, T.J.) 315–322 (Academic Press, 1990).
Gardes M, Bruns TD. ITS primers with enhanced specificity for basidiomycetes‐application to the identification of mycorrhizae and rusts. Mol. Ecol. 1993;2:113–118. doi: 10.1111/j.1365-294X.1993.tb00005.x. PubMed DOI
Edgar RC. UPARSE: highly accurate OTU sequences from microbial amplicon reads. Nat Meth. 2013;10:996–998. doi: 10.1038/nmeth.2604. PubMed DOI
Wang Q, Garrity GM, Tiedje JM, Cole JR. Naive Bayesian classifier for rapid assignment of rRNA sequences into the new bacterial taxonomy. Appl. Environ. Microb. 2007;73:5261–5267. doi: 10.1128/AEM.00062-07. PubMed DOI PMC
Schloss PD, et al. Introducing mothur: Open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl. Environ. Microb. 2009;75:7537–7541. doi: 10.1128/AEM.01541-09. PubMed DOI PMC