## 3 Results and Discussion
### Bacterial Community  
The Beta diversity reported in Figure 2a shows the generic distribution of microbial community considering the difference in the bacterial communities present in Naples and Pisa samples. The graphic highlights that the samples cluster in two well-defined groups, each representing an archaeological site. Alpha diversity, based on observed OTUs and on Shannon index, indicates the richness and the biodiversity of each sample community. Figure 2b shows the boxplot of Shannon index in the two sites. The median Shannon values for the two communities are similar but the index varies in a wider range for Naples samples. Sequencing results showed that the bacterial communities of almost all the analyzed samples were dominated by taxa belonging to the phyla Proteobacteria, Acidobacteria, and Plantomycetes (Figure 3a). It is interesting to observe that the community composition obtained with the two extraction methods for the same wood sample is always very similar. This suggests that the results obtained are not biased by an extraction limit and that it can be considered as representative of the actual microbial community. Proteobacteria accounted for more than 50% of the total reads in all the Naples samples, reaching 96% for \(N88\), and more than 30% for Pisa woods. The phylum Bacteroidetes was well represented in Naples communities, in some cases reaching relative frequencies of 10\(-\)20%, while it accounted for less than 5% in Pisa samples. The opposite results were registered for the phylum Chloroflexi. Figure 2: Diversity measures calculated on _16S_ rRNA gene sequencing data. (**a**) Beta diversity represented by Principle Coordinate Analysis Emperor plot on a Bray–Curtis distance matrix. Green dots: Naples, orange dots: Pisa. (**b**) Boxplots of Alpha-diversity Index (calculated as Shannon index) in the two archaeological sites. At class level (Figure S1), the communities of N samples were mainly composed of Gammaproteobacteria, Alphaproteobacteria, Planetomyectacia, and Bacteria with a neat prevalence of the first taxon. Instead, Alphaproteobacteria dominated in P samples and together with Gammaproteobacteria, Planetomyectacia, and Acidobacteria accounted for more than 60% of the whole communities. The communities of Naples samples were mainly composed of microorganisms belonging to the families Pseudomonas Pseudomonas (g. Pseudomonas), Burkholderiaceae (g. Janthinobacterium), Methylophilaceae, Pirellulaccae, and Xanthobacteraceae. Instead, the genera of the families Xanthobacteraceae (g. Pseudomonas), Caulobacteraceae, Solibacteraceae (g. Bryobacter), and Hyphomicrobiaceae (g. Hyphomicrobiome) were enriched in P samples (Figure S2 and Figure 3b). Even if the role of bacteria in the biodegradation of WAW is well-known and several studies investigated the degradation patterns produced by these microorganisms [8; 9; 11; 50; 51], very little is known about the bacterial genera involved in this phenomenon. Some of the genera identified during  
Figure 3: Stacked barcharts of the taxonomic profile at phylum (**a**) and genus (**b**) level. the present work (e.g., _Pseudomonas_, _Janthinobacterium_, _Flavobacterium_, _Brevundomonas_, _Sphingomonas_, and _Spirochaeta_) are known as members of the microbial community present in waterlogged wood and as active degraders of cellulose and/or lignin [22; 23; 24; 25; 29; 31]. _Pseudomonas_ sp. characterized the community of all the samples from Naples, reaching more than 40% of the relative frequency in N88, while the taxon was present only in four of the analyzed Pisa samples, always with frequencies lower than 0.5%. Microorganisms belonging to the genus _Pseudomonas_ are strict aerobes or facultative anaerbes. Some species are involved in denitrification or are implicated in sulfur and iron metabolism [23]. A study carried out on chips of _Eucalyptus grandis_\(\times\)_Eucalyptus urophyllla_, _Populus canadensis_, and _Larix olensis_ demonstrated that the strain _Pseudomonas_ sp.