Sampling site and sample collection
In order to detect the microbial diversity of the Dhala impact crater, we collected four samples and the details of the four samples (DM1, DM2, DM3, and DM4) are mentioned in the Supplementary Table 1. Among these four samples, DM1 (Coordinate: 25.29592761 N 78.1410341 E) and DM2 (Coordinate: 25.29502647 N 78.1407712 E) samples were collected from the top area (areas with no human or animals’ interference); while DM3 (Coordinate: 25.287780 N 78.141533 E) and DM4 (Coordinate: 25.298972 N 78.152861 E) samples were collected from the bottom area of the crater (areas with human or animals’ interference) (Supplementary Figure 1 and Supplementary Table 1). Therefore, the locations of the samples have major differences and we were able to characterize both common and differentially abundant microbial taxa in each samples.
Metagenomic extraction of DNA and microbial diversity analysis
Good quality DNA was obtained using the above mentioned DNA extraction procedure. Sequence datasets acquired after removal of low-quality sequences were trimmed, and only sequences of good quality were utilized for subsequent downstream analyses. A total of 23,68,428 high-quality sequences were obtained from all the four samples (Supplementary Table 1). Taxonomic assignment of these sequences to define operational taxonomic units (OTUs) was based on a similarity threshold of 97%. Good coverage (≥95%) indicated a high degree of sequence coverage (Supplementary Table 1). Highest OTUs (387) were found in the DM2 sample followed by DM3 sample (301) (Supplementary Table 1). The sequences were submitted to NCBI; the Accession Number and Bioproject details are shown in the Supplementary Table 1.
To evaluate community diversity characteristics of the microbial populations associated with the Dhala Impact Crater, we evaluated the alpha diversity within these four samples using non-parametric indicators (Shannon Index, Chao1 Index, Simpson Index, Inverse Simpson Index, and Species Count). Significant (P ≤ 0.05) differences were found in microbial community richness and evenness, keeping substantially higher diversity in the microbial niche of DM2 sample (Shannon Index = 4.257) followed by DM3 (Shannon Index = 4.246), DM4 (Shannon Index = 3.192), and DM1 (Shannon Index = 2.752) samples (Supplementary Figure 3A). Similar trend was also found in the case of the species dominance where highest diversity was found in the DM3 sample (Simpson Index = 0.96; Reverse Simpson Index = 25.17), however, total species richness was relatively higher in the DM1 and DM4 samples (Chao1 Index = 1946.5 and 1946.419, respectively) (Supplementary Figure 3A).
We consider that the sampling depth for our analysis was adequate to accurately characterize the microbial population since slope of the rarefaction curves became nearly asymptotic (Supplementary Figure 3B). Rarefaction curves of the number of observed species and sample size for each sample indicates that the recovered libraries from the DM2 and DM3 samples had greater species richness and abundance (Supplementary Figure 3B), being microbial communities more heterogeneous n these two samples compared to DM1 and DM4 samples. Overall all the non-parametric indicators of the alpha diversity analysis have indicated the presence of a significantly diverse microbial community in the Dhala Impact Crater.
Taxonomic analysis of the microbial community composition and structure
A total of 42 significantly abundant microbial phyla were detected in the Dhala Impact Crater samples out of which 26 most abundant phyla was common in all four samples that covered 61.9% of the total microbial diversity (Figure 1B). The principal coordinate analysis (PCA) conducted using the “plotPCA” package of the Galaxy open-source platform showed that microbial composition in the all four samples differed significantly but the DM2 and DM3 samples clustered together (Figure 1A), although they were collected from different elevation. Interestingly, DM1 and DM4 samples clustered separately but taxonomic analysis of these two samples have identified the presence of the relatively similar taxa in these two samples. PCA analysis of these four samples with other taxonomic categories also showed the similar trend (Figure 2A, 3A, 4A, and 6A). Therefore, the diversity of microbial population in the samples collected from the Dhala Impact Crater, was not directly dependent on the elevation of the sampling area. Significant diversity of the microbial populations was present in these samples but a direct correlation between the sample elevation and microbial diversity was not found.
Taxonomic analysis based on relative abundance revealed that out of the 26 commonly enriched phyla, Proteobacteria to be the most predominant phyla in the DM1 (90.09%) and DM4 (82.49%) samples (Figure 1C). On the contrary, Firmicutes were found to be most abundant in the case of the DM2 (28.39%) and DM3 (28.71%) followed by Planctomycetes (DM2 = 16.006%; DM3 = 17.20%) and Verrucomicrobia (DM2 = 8.05%; DM3 = 8.50%). Some phylum with low-abundance were uniquely present in some samples. For example, Poribacteria and Atribacteria were uniquely present in the DM3 and DM4 samples respectively (Supplementary Dataset 2).
Among the 45 most abundantly enriched microbial class (55.6% of the total identified microbial population) (Figure 2B), Gammaproteobacteria was most abundant in both DM1 (72.29%) and DM4 (73.16%) samples. In DM4 samples the Bacilli (11.95%) was the second most abundant class while in DM1 samples Betaproteobacteria (14.82%) holds the second position based on abundance (Figure 2C). However, DM2 and DM3 samples have shown significant difference compared to the other two samples. The class Clostridia have shown maximum abundance in the both DM2 (28.40%) and DM3 (28.67%) samples which was followed by Planctomycetia (DM2 = 14.65%; DM3 = 15.44%), Alphaproteobacteria (DM2 = 11.33%; DM3 = 11.42%), and Deltaproteobacteria (in DM2 = 9.55%) and Cytophagia (in DM3 = 10.50%) (Figure 2C). Interestingly, the class Lentisphaeria was uniquely present in the DM1 and DM2 samples while the class Endomicrobia was uniquely present in the DM3 and DM4 samples; however, these unique microbial classes have shown very low-abundance values (Supplementary Dataset 2).
Our taxonomic analysis has confirmed that 93.3% (total 28) microbial order were commonly present in these four samples (Figure 3B). More than half of the identified order (55.32%) belongs to the Pseudomandales in DM1 sample and in the DM4 samples Pseudomandales covered 35.94% which resulted it being the most abundant order in these two samples. Among other identified major taxa that was found in the two samples includes - Enterobacteriales (DM1 = 14.81%; DM4 = 26.11%), Burkholderiales (DM1 = 14.72%; DM4 = 5.74%), and Bacillales (DM1 = 5.01%; DM4 = 11.28%) (Figure 3B and Supplementary Dataset 2). On the contrary, Clostridiales (DM2 = 30.30%; DM3 = 30.53%) followed by Planctomycetales (DM2 = 15.65%; DM3 = 16.45%), and Cytophagales (DM2 = 8.16%; DM3 = 11.19%) – were the most abundantly present order in DM2 and DM3 samples (Figure 3B). Bdellovibrionales, Rhizobiales, Rhodospirillales, Sphingobacteriales, and Xanthomonadales have also showed relatively higher abundance in the case of the DM2 and DM3 samples (Supplementary Dataset 2). At the family level of taxonomic classification, a total of 26 OTUs were commonly enriched (Figure 4B). The family Pseudomonaceae in DM1 (44.37%) sample, and Enterobacteriace in DM4 (26.10%) samples were found to be most abundant while the family Clostridiaceae showed highest abundance in the case of the DM2 (27.92%) and DM3 (27.91%) samples (Figure 4C).
Figure 5 (A-D) is showing the combined representation of taxonomic composition and phylogenetic relationships among various genus identified in the four samples collected from the Dhala Impact Crater. Here, we have found that the Gammaproteobacteria and Betaproteobacteria were most abundant in the DM1 and DM4 samples; while Firmicutes followed by Alphaproteobacteria and Deltaproteobacteria were most abundant in the DM2 and DM4 samples. Therefore, this analysis confirmed that the phylum Proteobacteria and Firmicutes were ubiquitous and the most abundant microbial taxa across all the samples (Figure 5).
30 microbial species were whether commonly or uniquely enriched across all the samples (Figure 6B). A heatmap showing the relative abundance of these 30 microbial species were generated (Figure 6C). Pseudomonas sihuiensis, Ralstonia pickettii, Diplorickettsia massiliensis, Pseudomonas guguanensis, Acinetobacter baumannii, Enterobacter tabaci, and Pseudomonas stutzeri were the dominant species found in the DM1 and DM4 samples (Figure 6C). Bdellovibrio bacteriovorus, Sporocytophaga myxococcoides, Clostridium sensu stricto / C. swellfunianum, and Schlesneria paludicola were the most abundant microbial species found in the DM2 and DM3 samples (Figure 6C).
Interestingly, our analysis has found presence of the unclassified sequences, where 4.55% features were unknown (Supplementary Figure 4). This creates the possibility of identifying novel taxa from the soils of the Dhala Impact Crater. Overall, the assessment of taxonomic diversity analysis confirmed differences in the complexity of bacterial communities in these samples indicating the presence of a large microbial community in the Dhala Impact Crater.