Unraveling the microbiotas and key genetic contexts identified on stone heritage using illumina and nanopore sequencing platforms

Li, Qiang; Wu, Chao; He, Jintao; Zhang, Bingjian

doi:10.1016/j.ibiod.2023.105688

Cited by 3 publications

(4 citation statements)

References 79 publications

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“…Li and colleagues [30] used a WGA approach (Illumina + Nanopore) in biofilms thriving in Leshan and Feilaifeng stone cultural heritage sites. They were able to understand the biofilms' taxonomic profiles, while also gathering a strong knowledge of the microbial groups and gene families contributing to elemental nitrogen and sulfur metabolism enhancing stone biodeterioration.…”

Section: Application Of Oxford Nanopore ® In Cultural Heritage Biodet...mentioning

confidence: 99%

“…On the other hand, while a considerable number of studies employing the sequencer have been conducted with a WGA approach (Table 1), solely the works of Li and colleagues [30] and Nir and colleagues [31] dwelled deeper in the biodeteriorative metabolism potential from the metagenomic analysis data obtained. In the first work, this approach allowed to deeply understand metabolic pathways contributions to biogeochemical N and S cycling, known to deeply enhance stone biodeterioration [50].…”

Section: Biodeteriorative Metabolic Insightsmentioning

confidence: 99%

“…The cultural heritage resistome, i.e., the antimicrobial resistance genes (AMR or ARGs) of a community, is a topic gaining some recent focus on the area [30,56,57]. Studies on AMR genes on cultural heritage monuments and relics can be considered of great relevance, considering that they can allow to understand anthropogenic activity impacts, to monitor resistance to preservation/conservation efforts, to understand contamination source tracking and even to contribute to public health management [30,56,57].…”

Section: Cultural Heritage Resistomementioning

confidence: 99%

“…Li and colleagues [30] used both the Illumina and the Oxford Nanopore ® techniques to understand the microbiome and key genetic contexts from Leshan and Feilaifeng stone heritages. The authors applied the Oxford Nanopore ® sequencer for the first time in this context, and found high abundances and diversity of antibacterial biocide and metal resistance genes to copper and quaternary ammonium compounds.…”

Section: Cultural Heritage Resistomementioning

confidence: 99%

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Future Perspectives on the Application of the Oxford Nanopore® MinION™ Sequencer in Cultural Heritage Biodeterioration Studies

Trovão,

Soares

2024

Preprint

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The present work provides an updated overview of the application of the Oxford Nanopore® MinION™ sequencer in cultural heritage biodeterioration studies, while also providing a holistic discussion of possible future perspectives for their utilization in this research field. Due to the peculiar characteristics of this device, the last few years have seen the steady rise on the application of this system in a variety of cultural heritage materials, having been useful to understand microbial biodeteriogens diversity and some of their metabolic and biodeteriogenic features. Considering the immense potential for application of this system, this manuscript discusses further possibilities of the technique aiming to help understand critical questions on the cultural heritage biodeterioration area. Its application in various differential contexts, has opened the doors for their putative usage on other interesting sub-areas of research worthy of future investigations, including: biodeteriogens genome and transcriptome analysis, metatranscriptomics, biodeteriorative metabolism studies, inter and intra kingdom interactions analysis, resistome profiling, object history and context studies, in situ applications, bioprospecting and biotechnology.

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Section: Application Of Oxford Nanopore ® In Cultural Heritage Biodet...mentioning

confidence: 99%

Section: Biodeteriorative Metabolic Insightsmentioning

confidence: 99%

Section: Cultural Heritage Resistomementioning

confidence: 99%

Section: Cultural Heritage Resistomementioning

confidence: 99%

See 2 more Smart Citations

Future Perspectives on the Application of the Oxford Nanopore® MinION™ Sequencer in Cultural Heritage Biodeterioration Studies

Trovão,

Soares

2024

Preprint

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Microbiome shifts elicited by ornamental lighting of granite facades identified by MinION sequencing

Méndez,

Maisto,

Pavlović

et al. 2024

Journal of Photochemistry and Photobiology B: Biology

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Red sandstone surface microbiota: functional convergence despite taxonomic divergence under dispersal limitation and hetero selection

Wang,

Zhu,

Wang

et al. 2024

Preprint

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Understanding the role of microbiota on stone surfaces is essential for developing effective grottoes conservation strategies. However, ecological feature of microbial communities on stone surfaces remains underexplored. In this study, we explored diversity, ecological feature, and functional profiles of microbial communities on the red sandstone surface of the Leshan Giant Buddha from microbial ecology perspective. The results show that Proteobacteria, Actinobacteria, and Cyanobacteria are the dominant prokaryotic phyla, and Ascomycota is the most dominant eukaryotic phylum. Interestingly, despite taxonomic divergence, the functional profiles of different types of the microbial communities remain convergent across all samples. As indicated by the ecological modelling, the interplay of dispersal limitation and hetero selection might have contributed to such species divergence, while selective pressure from the harsh environment on the stone surface promoted functional convergence. The assembly of visually distinct microbial communities is linked to a narrower ecological niche, higher proportion of habitat specialists, elevated complexity, and increased resilience of the prokaryotic network to disturbances. Microbial-mediated ammonium assimilation and nitrogen mineralization might be the two prominent processes that contribute to stone biodeterioration. This study deepens our understanding of microbial community assembly mechanism on stone cultural heritage surfaces and functional potentials, which provides microbial ecological insights for the conservation of these cultural treasures.

show abstract

Unraveling the microbiotas and key genetic contexts identified on stone heritage using illumina and nanopore sequencing platforms

Cited by 3 publications

References 79 publications

Future Perspectives on the Application of the Oxford Nanopore® MinION™ Sequencer in Cultural Heritage Biodeterioration Studies

Future Perspectives on the Application of the Oxford Nanopore® MinION™ Sequencer in Cultural Heritage Biodeterioration Studies

Microbiome shifts elicited by ornamental lighting of granite facades identified by MinION sequencing

Red sandstone surface microbiota: functional convergence despite taxonomic divergence under dispersal limitation and hetero selection

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