Application of metagenomic methods for selection of an optimal growth medium for bacterial diversity analysis of microbiocenoses on historical stone surfaces

Dyda, Magdalena; Decewicz, Przemysław; Romaniuk, Krzysztof; Wojcieszak, Martyna; Skłodowska, Aleksandra; Dziewit, Łukasz; Drewniak, Łukasz; Laudy, Agnieszka E.

doi:10.1016/j.ibiod.2017.03.009

Cited by 22 publications

(12 citation statements)

References 39 publications

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“…The analyses of the Rotunda microbiome were carried out with the use of the high-throughput sequencing of commonly acknowledged diversity markers –16S rDNA gene and ITS fragments that have been successfully employed previously in the characterization of museum and historic buildings [6,22,23,24,25] and for many years have routinely been used in microbiome studies of biogas systems [26,27,28], aquatic habitats [29,30], soils [31,32], intestinal tracts [33,34], and many other environments [35,36].…”

Section: Discussionmentioning

confidence: 99%

Bacterial and Fungal Diversity Inside the Medieval Building Constructed with Sandstone Plates and Lime Mortar as an Example of the Microbial Colonization of a Nutrient-Limited Extreme Environment (Wawel Royal Castle, Krakow, Poland)

Dyda

Pyzik

Wilkojc³

et al. 2019

Microorganisms

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Biodeterioration is a serious threat to cultural heritage objects and buildings. The deterioration of a given material often incurs irreparable losses in terms of uniqueness and historical value. Hence preventive actions should be taken. One important challenge is to identify microbes involved in the biodeterioration process. In this study, we analyzed the microbial diversity of an ancient architectonical structure of the Rotunda of Sts. Felix and Adauctus, which is a part of the Wawel Royal Castle located in Krakow, Poland. The Rotunda is unavailable to tourists and could be treated as an extreme habitat due to the low content of nutrients coming either from sandstone plates bound with lime mortar or air movement. Microbial diversity was analyzed with the use of the high-throughput sequencing of marker genes corresponding to fragments of 16S rDNA (for Bacteria) and ITS2 (internal transcribed spacer 2) (for Fungi). The results showed that the microbial community adhered to wall surfaces is, to a large extent, endemic. Furthermore, alongside many microorganisms that could be destructive to masonry and mortar (e.g., Pseudomonas, Aspergillus), there were also bacteria, such as species of genera Bacillus, Paenisporosarcina, and Amycolatopsis, that can positively affect wall surface properties by reducing the damage caused by the presence of other microorganisms. We also showed that airborne microorganisms probably have little impact on the biodeterioration process as their abundance in the microbial community adhered to the ancient walls was very low.

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Section: Discussionmentioning

confidence: 99%

Bacterial and Fungal Diversity Inside the Medieval Building Constructed with Sandstone Plates and Lime Mortar as an Example of the Microbial Colonization of a Nutrient-Limited Extreme Environment (Wawel Royal Castle, Krakow, Poland)

Dyda

Pyzik

Wilkojc³

et al. 2019

Microorganisms

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“…For the DNA extracted from the bacteria grown on each type of medium, PCRs were conducted in triplicate and then mixed. The PCRs were prepared and performed as described previously [20]. The PCR products were quality-checked using electrophoresis in a 1.5% agarose gel.…”

Section: Metagenomic Dna Isolation and Sequencingmentioning

confidence: 99%

Assessment of Bacterial Contamination of Air at the Museum of King John III’s Palace at Wilanow (Warsaw, Poland): Selection of an Optimal Growth Medium for Analyzing Airborne Bacteria Diversity

et al. 2020

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There is no standardized protocol for the assessment of microbial air contamination in museums and other cultural heritage sites. Therefore, most museums conduct such assessments based on their own guidelines or good practices. Usually, microbial air contamination is assessed using only classical microbiology methods with the application of a single growth medium. Therefore, this medium should be carefully selected to limit any selective cultivation bias. Metabarcoding, i.e., a next-generation sequencing (NGS)-based method, combined with classical microbiological culturing was used to assess the effectiveness of various media applications in microbiological screening at the Museum of King John III’s Palace at Wilanow (Warsaw, Poland). The obtained results indicated that when using a classical microbiology approach to assess the microbial air contamination at the museum, the selection of a proper growth medium was critical. It was shown that the use of rich media (commonly applied by museum conservators) introduced significant bias by severely underreporting putative human pathogens and the bacterial species involved in biodeterioration. Therefore, we recommend the use of other media, such as Frazier or Reasoner’s 2A (R2A) medium, as they could yield more diverse communities and recovered the highest number of genera containing human pathogens, which may be suitable for public health assessments.

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“…An analysis of urban soils from the street green belts of the city of Chicago, USA, revealed that soils along a one‐way street showed higher Shannon and phylogenetic diversities than other soils, including those along a two‐way street, a feature that could be correlated with soil pH, moisture and texture (Wang et al ., ). We believe that the microorganisms living in the street, in street gutters and on pedestrian surfaces may present specific surface‐associated diversity, such as the ones identified on concrete (Domingo et al ., ; Li et al ., ; Gomez‐Alvarez et al ., ; Jiang et al ., ; Cayford et al ., ; Cowle et al ., ; Li et al ., ) or buildings and monuments (Ragon et al ., ; Chimienti et al ., ; Gaylarde et al ., ; Adamiak et al ., ; Dyda et al ., ).…”

Section: Introductionmentioning

confidence: 97%

Analysis of interdomain taxonomic patterns in urban street mats

Hervé

Lopez

2020

Environmental Microbiology

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Summary Streets are constantly crossed by billions of vehicles and pedestrians. Their gutters, which convey stormwater and contribute to waste management, and are important for human health and well‐being, probably play a number of ecological roles. Street surfaces may also represent an important part of city surface areas. To better characterize the ecology of this yet poorly explored compartment, we used filtration and DNA metabarcoding to address microbial community composition and assembly across the city of Paris, France. Diverse bacterial and eukaryotic taxonomic groups were identified, including members involved in key biogeochemical processes, along with a number of parasites and putative pathogens of human, animals and plants. We showed that the beta diversity patterns between bacterial and eukaryotic communities were correlated, suggesting interdomain associations. Beta diversity analyses revealed the significance of biotic factors (cohesion metrics) in shaping gutter microbial community assembly and, to a lesser extent, the contribution of abiotic factors (pH and conductivity). Co‐occurrences analysis confirmed contrasting non‐random patterns both within and between domains of life, specifically when comparing diatoms and fungi. Our results highlight microbial coexistence patterns in streets and reinforce the need to further explore biodiversity in urban ground transportation infrastructures.

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Application of metagenomic methods for selection of an optimal growth medium for bacterial diversity analysis of microbiocenoses on historical stone surfaces

Cited by 22 publications

References 39 publications

Bacterial and Fungal Diversity Inside the Medieval Building Constructed with Sandstone Plates and Lime Mortar as an Example of the Microbial Colonization of a Nutrient-Limited Extreme Environment (Wawel Royal Castle, Krakow, Poland)

Bacterial and Fungal Diversity Inside the Medieval Building Constructed with Sandstone Plates and Lime Mortar as an Example of the Microbial Colonization of a Nutrient-Limited Extreme Environment (Wawel Royal Castle, Krakow, Poland)

Assessment of Bacterial Contamination of Air at the Museum of King John III’s Palace at Wilanow (Warsaw, Poland): Selection of an Optimal Growth Medium for Analyzing Airborne Bacteria Diversity

Analysis of interdomain taxonomic patterns in urban street mats

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