## 2 Materials and Methods  
### Location and Sampling  
The Church of Trofa or Church of Sao Salvador da Trofa (Figure 1a) is a Catholic temple located in Trofa (Trofa do Vouga), in the Portuguese district of Aveiro, Agueda county (N 40 36.653 \({}^{\prime}\) W 008 28.729). This church houses the Lemos Pantheon (Figure 1b,c), a remarkable Renaissance sculptural ensemble dating from the 16 th century, carved in white Anca limestone, and attributed to the artist [PERSON]. Commissioned by [PERSON] in 1534, the Lemos Pantheon presents itself as a burial place for the ancestors of the third lord of Trofa. It integrates two tombstone groups facing each other, both formed by two arches separated by pilasters and topped by an entablature. On the right-hand side are the tombs of the first lords of Trofa, [PERSON] and his son, [PERSON], and their respective wives, [PERSON] and [PERSON], leaving the men in the arch nearest the altar. On the opposite side lies buried [PERSON], wife of the founder, and in the arch closest to the altar [PERSON], with a praying statue [43].  
The Church of Trofa, comprising the tombs of the [PERSON] family, has been classified as a National Monument since 1992 (IPA.00001042, decree of 16-06-1910, DG, nr 136, of 23-06-1910). More details about the monument, including photographs, can be accessed on the SIPA website [43], an online information and documentation system on the Portuguese architectural, urban and landscape heritage managed by the General Directorate for Cultural Heritage (DGPC). Despite being the most important local landmark, it is mainly used for local religious events. In general, the tomb complex is in a reasonable state of conservation; however, some areas present visible pathologies, severely affecting the limestone of this site both structurally and aesthetically.  
All samples were collected indoors in July 2021, during the summer season. A digital thermohygrometer was used to measure the temperature (T) and relative humidity (RH) inside, at the beginning and the end of the sampling procedure. The average values were T 22 \({}^{\circ}\)C and RH 51%. After careful observation, sampling was carried out on representative areas showing clear evidence of alteration and degradation. Four samples were collected from these areas (Figure 2) and distinct biodeterioration outlines found in these sites were classified based in the ICOMOS Illustrated glossary on stone deterioration patterns: L1--dark and green biofilm (DGB), L2--green biofilm (GB), L3--black discoloration (BD) and L4--salt efflorescence (SE) [44]. Microinvasive sampling using sterile scalpels by scrapping small areas (approximately 0.5 g) into a sterile petri dish, as well as noninvasive sampling by swabing surfaces with sterile nitrocellulose discs (\(\O\) 5 cm, 2 per sampling area) were carried out.  
Figure 1: Study site (**a**) Church of Trofa do Vouga which houses the Lemos Pantheon. (**b**) Left side of the Pantheon comprising the tombs of [PERSON] (on the right) and her husband, [PERSON] (on the left), where the praying statue stands (**c**) Right side of the Pantheon comprising the tombs of [PERSON] and his son, [PERSON] (on the right), and their wives, [PERSON] and [PERSON], respectively (on the left).  
Each collected sample (L1 to L4) was divided into two aliquots (each with \(\approx\)0.25 g and 1 disc): one for Illumina high-throughput sequencing, stored at \(-\)80 \({}^{\circ}\)C until further processing; and the other for direct fungal isolation, stored in the dark, at room temperature and processed within 4 h of collection.