Nanopore Sequencing and Bioinformatics for Rapidly Identifying Cultural Heritage Spoilage Microorganisms
Microbiological methodologies allow understanding the causes that lead to the development of a certain microbial community colonizing an artistic surface, to characterize its composition and describe its role in the deterioration of the constituent materials. Metagenomics allows identifying microbia...
| Main Authors: | , , , , , , , |
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| Format: | Article |
| Language: | English |
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Frontiers Media S.A.
2020-02-01
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| Series: | Frontiers in Materials |
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| Online Access: | https://www.frontiersin.org/article/10.3389/fmats.2020.00014/full |
| _version_ | 1828775927064035328 |
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| author | Alessandro Grottoli Alessandro Grottoli Marzia Beccaccioli Marzia Beccaccioli Emma Zoppis Rosita Silvana Fratini Emily Schifano Maria Laura Santarelli Daniela Uccelletti Massimo Reverberi Massimo Reverberi |
| author_facet | Alessandro Grottoli Alessandro Grottoli Marzia Beccaccioli Marzia Beccaccioli Emma Zoppis Rosita Silvana Fratini Emily Schifano Maria Laura Santarelli Daniela Uccelletti Massimo Reverberi Massimo Reverberi |
| author_sort | Alessandro Grottoli |
| collection | DOAJ |
| description | Microbiological methodologies allow understanding the causes that lead to the development of a certain microbial community colonizing an artistic surface, to characterize its composition and describe its role in the deterioration of the constituent materials. Metagenomics allows identifying microbial communities directly in their natural environments, bypassing the need for isolation and cultivation of individual species, thus providing a more comprehensive picture of the biodiversity present on a surface compared with standard cultivation methods. Furthermore, molecular analyses require small amounts of material, favoring the preservation of the artistic surface during sampling. Here, we verified the suitability of a protocol consisting in DNA extraction with micro-invasive sampling, using adhesive tape, PCR amplification with universal primers [bacteria (16S), fungi (ITS), and Viridiplantae (18S)], and amplicon sequencing by Oxford Nanopore Technologies (ONT) in the hypogeum of Basilica di San Nicola in Carcere Church (Rome, Italy). Sequence data were analyzed with a bioinformatic pipeline customized for pinpointing cultural heritage spoiling organisms, named “AmpLIcon SequencIng Analysis” (ALISIA). These data were integrated with traditional microbiology techniques that allowed the isolation of cultivable bacteria; three species were also characterized through their capability of biofilm formation and antibiotic resistance. Further, Fourier-transform infrared spectroscopy (FTIR) spectroscopy was performed to characterize the main products present on the masonry surface providing indications on the type of decay present. This novel biological workflow represents a powerful opportunity to investigate the microbial colonization of artistic surfaces aimed at implementing preservation strategies of cultural heritage from bio-spoilage. |
| first_indexed | 2024-12-11T15:48:01Z |
| format | Article |
| id | doaj.art-a4f3516e178b4bfa807c7ce3beaa054f |
| institution | Directory Open Access Journal |
| issn | 2296-8016 |
| language | English |
| last_indexed | 2024-12-11T15:48:01Z |
| publishDate | 2020-02-01 |
| publisher | Frontiers Media S.A. |
| record_format | Article |
| series | Frontiers in Materials |
| spelling | doaj.art-a4f3516e178b4bfa807c7ce3beaa054f2022-12-22T00:59:38ZengFrontiers Media S.A.Frontiers in Materials2296-80162020-02-01710.3389/fmats.2020.00014506398Nanopore Sequencing and Bioinformatics for Rapidly Identifying Cultural Heritage Spoilage MicroorganismsAlessandro Grottoli0Alessandro Grottoli1Marzia Beccaccioli2Marzia Beccaccioli3Emma Zoppis4Rosita Silvana Fratini5Emily Schifano6Maria Laura Santarelli7Daniela Uccelletti8Massimo Reverberi9Massimo Reverberi10SARA EnviMob s.r.l., Rome, ItalyDepartment of Environmental Biology, Sapienza University of Rome, Rome, ItalySARA EnviMob s.r.l., Rome, ItalyDepartment of Environmental Biology, Sapienza University of Rome, Rome, ItalyDepartment of Biology and Biotechnology Charles Darwin, Sapienza University of Rome, Rome, ItalyDepartment of Environmental Biology, Sapienza University of Rome, Rome, ItalyDepartment of Biology and Biotechnology Charles Darwin, Sapienza University of Rome, Rome, ItalyDepartment of Chemical Engineering Materials Environment, Sapienza University of Rome, Rome, ItalyDepartment of Biology and Biotechnology Charles Darwin, Sapienza University of Rome, Rome, ItalySARA EnviMob s.r.l., Rome, ItalyDepartment of Environmental Biology, Sapienza University of Rome, Rome, ItalyMicrobiological methodologies allow understanding the causes that lead to the development of a certain microbial community colonizing an artistic surface, to characterize its composition and describe its role in the deterioration of the constituent materials. Metagenomics allows identifying microbial communities directly in their natural environments, bypassing the need for isolation and cultivation of individual species, thus providing a more comprehensive picture of the biodiversity present on a surface compared with standard cultivation methods. Furthermore, molecular analyses require small amounts of material, favoring the preservation of the artistic surface during sampling. Here, we verified the suitability of a protocol consisting in DNA extraction with micro-invasive sampling, using adhesive tape, PCR amplification with universal primers [bacteria (16S), fungi (ITS), and Viridiplantae (18S)], and amplicon sequencing by Oxford Nanopore Technologies (ONT) in the hypogeum of Basilica di San Nicola in Carcere Church (Rome, Italy). Sequence data were analyzed with a bioinformatic pipeline customized for pinpointing cultural heritage spoiling organisms, named “AmpLIcon SequencIng Analysis” (ALISIA). These data were integrated with traditional microbiology techniques that allowed the isolation of cultivable bacteria; three species were also characterized through their capability of biofilm formation and antibiotic resistance. Further, Fourier-transform infrared spectroscopy (FTIR) spectroscopy was performed to characterize the main products present on the masonry surface providing indications on the type of decay present. This novel biological workflow represents a powerful opportunity to investigate the microbial colonization of artistic surfaces aimed at implementing preservation strategies of cultural heritage from bio-spoilage.https://www.frontiersin.org/article/10.3389/fmats.2020.00014/fullnanoporebioinformaticmicrobial communityartistic surfacesnon invasive approach |
| spellingShingle | Alessandro Grottoli Alessandro Grottoli Marzia Beccaccioli Marzia Beccaccioli Emma Zoppis Rosita Silvana Fratini Emily Schifano Maria Laura Santarelli Daniela Uccelletti Massimo Reverberi Massimo Reverberi Nanopore Sequencing and Bioinformatics for Rapidly Identifying Cultural Heritage Spoilage Microorganisms Frontiers in Materials nanopore bioinformatic microbial community artistic surfaces non invasive approach |
| title | Nanopore Sequencing and Bioinformatics for Rapidly Identifying Cultural Heritage Spoilage Microorganisms |
| title_full | Nanopore Sequencing and Bioinformatics for Rapidly Identifying Cultural Heritage Spoilage Microorganisms |
| title_fullStr | Nanopore Sequencing and Bioinformatics for Rapidly Identifying Cultural Heritage Spoilage Microorganisms |
| title_full_unstemmed | Nanopore Sequencing and Bioinformatics for Rapidly Identifying Cultural Heritage Spoilage Microorganisms |
| title_short | Nanopore Sequencing and Bioinformatics for Rapidly Identifying Cultural Heritage Spoilage Microorganisms |
| title_sort | nanopore sequencing and bioinformatics for rapidly identifying cultural heritage spoilage microorganisms |
| topic | nanopore bioinformatic microbial community artistic surfaces non invasive approach |
| url | https://www.frontiersin.org/article/10.3389/fmats.2020.00014/full |
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