Distribution and Diversity of Bacteria and Fungi Colonization in Stone Monuments Analyzed by High-Throughput Sequencing

Abstract

The historical and cultural heritage of Qingxing palace and Lingyin and Kaihua temple, located in Hangzhou of China, include a large number of exquisite Buddhist statues and ancient stone sculptures which date back to the Northern Song (960–1219 A.D.) and Qing dynasties (1636–1912 A.D.) and are considered to be some of the best examples of ancient stone sculpting techniques. They were added to the World Heritage List in 2011 because of their unique craftsmanship and importance to the study of ancient Chinese Buddhist culture. However, biodeterioration of the surface of the ancient Buddhist statues and white marble pillars not only severely impairs their aesthetic value but also alters their material structure and thermo-hygric properties. In this study, high-throughput sequencing was utilized to identify the microbial communities colonizing the stone monuments. The diversity and distribution of the microbial communities in six samples collected from three different environmental conditions with signs of deterioration were analyzed by means of bioinformatics software and diversity indices. In addition, the impact of environmental factors, including temperature, light intensity, air humidity, and the concentration of NO2 and SO2, on the microbial communities’ diversity and distribution was evaluated. The results indicate that the presence of predominantly phototrophic microorganisms was correlated with light and humidity, while nitrifying bacteria and Thiobacillus were associated with NO2 and SO2 from air pollution.

Tales from the tomb: the microbial ecology of exposed rock surfaces

“…Likewise, the eukaryotic taxa we found to be common on tombstone surfaces have previously been observed on rock surfaces. Similar to other studies of rock colonizing fungi, the fungi we found were all from the phylum Ascomycota (Li et al ., ). Of these taxa, two orders ( Chaetothyriales and Capnodiales ) include members known as black melanized micro‐colonial fungi (MCF), which live within subaerial biofilms on rock and have been found in desert varnish (Gorbushina, ; Northup et al ., ).…”

“…1) have been observed previously in comparable environments such as stone monuments. Bacteria within the genera Sphingomonas, Hymenobacter, Spirosoma, Truepera, Pseudonocardia, the family Acetobacteraceae and the phyla Acidobacteria and FBP were found on the surface of stone monuments in China (Li et al, 2016). Several of these bacterial groups have also been identified from dust samples (Sphingomonas, Hymenobacter, Pseudonocardiaceae, Sporichthyaceae, Acetobacteraceae), which may explain their global ubiquity on rock surfaces (Favet et al, 2013).…”

Polyphasic insights into the microbiomes of the Takamatsuzuka Tumulus and Kitora Tumulus

“…Many studies have investigated the causes of biodeterioration of cultural heritage sites using cultureindependent methods, e.g., 16S rRNA gene sequence, PCR-DGGE, clone library, and NGS analyses Cheeptham, 2013;Engle, 2015;Gurtner et al, 2000;Li et al, 2016;Saiz-Jiménez, 2003, 2015Schabereiter-Gurtner et al, 2002a;Zengler, 2008). In particular, culture-independent methods have been used to analyze the microbial communities of the Lascaux Cave in France, the Altamira Cave in Spain, and the necropolis in Italy (Bastian et al, 2009a(Bastian et al, , 2009c(Bastian et al, , 2010Diaz-Herraiz et al, 2013;Garcia-Anton et al, 2014;Martin-Sanchez and Saiz-Jiménez, 2014;Saiz-Jiménez, 2014;SchabereiterGurtner et al, 2002b).…”

Assessment of microbiota present on a Portuguese historical stone convent using high‐throughput sequencing approaches

“…Small subunit ribosomal DNA genes like 16S and 18S universally present in all prokaryotes and eukaryotes, respectively, provide an efficient mean to identify microorganisms. These ribosomal sequences possess variable and highly conserved regions, which are used as phylogenetic markers to identify and distinguish the different microorganisms on all phylogenetic levels (Dakal & Arora, 2012; Kennedy & Clipson, 2003; Li, Zhang, He, & Yang, 2016; Zhang, Ping, Zhou, Wang, & Zhang, 2018). The internal transcribed spacer (ITS) region is also an effective tool for the identification of eukaryotic population (Anderson & Cairney, 2004; Dakal & Arora, 2012; Kennedy & Clipson, 2003).…”

“…Other nucleic acid approaches can be applied to detect uncultivable microorganisms. Recent developments in sequencing chemistries, bioinformatics, and automated instruments have revolutionized the knowledge of microbial diversity (Dyda et al, 2018; Edgar, Haas, Clemente, Quince, & Knight, 2011; England & Pettersson, 2005; Li et al, 2016; Mardis, 2008; Schubert, Lindgreen, & Orlando, 2016; Shendure & Ji, 2008; Zhang, Chiodini, Badr, & Zhang, 2011; Zhang et al, 2018; Zhou et al, 2015). The ongoing advances in genomics and sequencing technologies are allowing a new era of microbial community analyses using culture‐independent approaches such as metagenomics, metaproteomics, metatranscriptomics, and proteogenomics which are fundamental for the full identification of the microbial diversity and to understand their interactions with biotic and abiotic factors (Rastogi & Sani, 2011).…”