*3.1. Analysis of Essential Parameters and Taxonomic Hit Distribution*

Out of seven analyzed samples, five belong to *L. baikalensis* (three healthy and two bleached samples) and *B. intermedia* (one healthy and one bleached sample). Sequences were deposited in the NCBI-SRA portal (PRJNA665339). The basic nucleotide features (Base pair and total sequence count) of the selected samples are shown in Table 1.

We performed a taxonomic hits distribution of taxa using a contigLCA algorithm finding a single consensus taxonomic entity for all features on each individual sequence. The bacterial community was dominated by Chlorophyta, Acidobacteria, Bacteroidetes, Actinobacteria and Cyanobacteria as shown in Figure 1a. It shows that the overall 21 phyla play a major role in the growth physiology and maintenance of their cell survivability in freshwater environments. Samples LBH3 and BIH1 have a high relative abundance of Chlorophyta (80%) while this is 50% or less in other samples. Acidobacteria, Proteobacteria, Bacteroidetes, Cyanobacteria and Actinobacteria are found to be abundant and distributed nonspecifically between healthy and bleached samples (Figure 1b).

**Figure 1.** A phylum based bar diagram represents overall reads (**a**) and separated bacterial reads (**b**) classification was predicted among healthy and bleached freshwater sponges *Lubomirskia baikalensis* and *Baikalospongia intermedia*.

### *3.2. Analysis of Rarefaction Curve*

The rarefaction curve plot was used to annotate the species richness among the samples. From our analysis, we identified that the species count is increased in bleached samples of *L. baikalensis* (LBB1) upon 360,000 sequence reads. Whereas LBH3 has increased its species count to 1000 within a short number of sequence reads (250,000). It clearly indicates that a larger amount of bacterial diversity was found in the LBH3 sample. Whereas other samples have 600–800 species count within a short read. The samples LBH2 are found to be a low species diversity sample (Figure 2). Bacterial diversity increases in bleached samples of *B. intermedia*.

**Figure 2.** A phylum based rare-fraction curve was predicted among healthy and bleached fresh-water sponges *Lubomirskia baikalensis* and *Baikalospongia intermedia*.

#### *3.3. Analysis of Relative Abundances of OTUs at Genus Level*

The genus based rank abundance and operational taxonomic units were computed for top hits from the selected samples. It shows that a predominance of bacterial genera, such as *Flavobacterium*, *Eubacterium, Candidadus* and *Tetrasphaera,* are found to be abundant in a healthy sample of *L. Baikalensis* (LBH1), while *Synechococcus* was highly abundant in *L. baikalensis* (LBH2). While compared to the bleached samples, few genera, such as *Nitrospira*, *Planctomyces*, *Prolixibacter* and *Clostridium,* are found to be abundant (Figure 3a). We further compared the top 50 relative abundance genera; it shows that the overall 16 genera are commonly found in both healthy and bleached *L. baikalensis* samples (Figure 3b). Whereas 30 common and 20 unique genera are found in two healthy *L. baikalensis* samples (LBH1 and LBH2) (Figure 3c).

**Figure 3.** Top hits rank abundance plot comparison based on genus-level for selected healthy and bleached sponges. (**a**) The heat map represents the abundances of annotations of taxonomic richness and evenness on a log scale. (**b**,**c**) The Venn diagram represents the common and unique genus found in the samples.
