Geochemical properties of soil samples
The main chemical parameters of the pooled soil samples from different climatic zones (TWCZ, ACZ, HSCZ and MCZ) were analyzed and notable differences were observed in the values of pH and moisture content. The moisture content percentage was recorded highest (13.06%) in TWCZ and lowest (0.07%) in ACZ. The pH was recorded lowest (3.94) in TWCZ compared to ACZ (8.05) and HSCZ (8.13), which were mildly alkaline. MCZ showed a mildly acidic nature (5.44) with a moderate pH value. Total organic carbon (TOC) values did not show any drastic difference and were highest for MCZ. The values of nitrogen (17.00%), calcium (6.07%), magnesium (2.43%), phosphorus (0.08%), iron (1.26%), and boron (15.12 ppm) were recorded highest in ACZ compared to other climatic zones. There was lesser difference in TOC, potassium, phosphorous, iron, and boron values among the other climatic zones. A considerable difference was observed in the values of calcium (1.8%) and magnesium (0.4), which was recorded lowest in HSCZ compared to the other climatic zones (Additional file 2).
Bacterial diversity correlation with soil profile and climatic factors
The correlation analysis revealed that H’ (Shannon diversity) index, S (species richness), OTU abundance were positively correlated with moisture, TOC, K, MAP (mean annual precipitation), with a strong positive correlation between S and K. On the other hand, a negative correlation was observed with pH, Ca, N, B. Fe, P, Mg and MAT (mean annual temperature) with a very strong negative correlation between H’ and Fe (Additional file 3). The p value for Fe (p>0.05) showed a significant correlation with diversity parameters (Additional file 4).
Read characteristics and bacterial diversity parameters
A total of 132130 high-quality reads were obtained from the four contrasting climatic zones that were assigned to 16556 bacterial OTUs. The maximum number of reads was obtained in TWCZ, and the minimum number of reads was obtained in ACZ. Similarly, TWCZ also had the highest number (5694) of OTUs, whereas ACZ had the lowest number (841) of OTUs among the zones. The species diversity (different species) and richness (no. of different kinds) were highest in HSCZ and lowest in ACZ. The species evenness (closeness of species) was highest in HSCZ and lowest in TWCZ (Table 1). There was not much difference in the diversity indices (H’, D) among the zones except for ACZ.
Table 1 Alpha diversity parameters of the four contrasting climatic zones. The bacterial species diversity and richness was maximum in HSCZ and minimum in ACZ.
Climatic zones
|
TWCZ
|
ACZ
|
HSCZ
|
MCZ
|
Reads obtained
|
69485
|
16684
|
57899
|
57547
|
OTUs Assigned
|
5694
|
841
|
5122
|
4899
|
Shannon-wiener diversity index (H’)
|
7.371
|
6.678
|
7.449
|
7.254
|
Simpsons diversity index (D)
|
0.998
|
0.997
|
0.998
|
0.998
|
Species richness (Margalef)
|
301.041
|
150.476
|
303.234
|
260.940
|
Species evenness (Pielou)
|
0.916
|
0.921
|
0.927
|
0.920
|
Taxonomic abundance and bacterial diversity
The classified sequences (known taxonomy) obtained from all the four contrasting climatic zones were affiliated with eighteen different phyla (Additional file 5), which was further narrowed down to the top eight phyla based on the relative percentage abundance and the rest of the phyla were grouped into others that showed less than 0.2% relative abundance. Amongst these eight phyla, Firmicutes appeared as the most dominant phylum followed by Proteobacteria, Actinobacteria, Planctomycetes, Acidobacteria, Bacteroidetes, Verrucumicrobia, and Cyanobacteria. Surprisingly, the phylum Firmicutes, which was dominant (>30%) in all other zones, was less abundant (<7%) in MCZ. Proteobacteria was more dominant in MCZ compared to Firmicutes. HSCZ showed a stable abundance pattern (34.82%, 14.43%, 11.16%, 4.37%, 1.43%, 0.56%, 0.43% and 0.21%) for all these eight phyla compared to other zones. Contrastingly, the abundance of Cyanobacteria was more in ACZ compared to the other zones. Firmicutes mostly dominated TWCZ with a lower percentage of unclassified bacterial phyla, which was seen as high in MCZ (Fig. 1). Other phyla that were observed in lower percentage among the top abundant were Bacteroidetes, Acidobacteria, Verrucumicrobia, and Cyanobacteria, in which abundance of Cyanobacteria was high in ACZ amongst other zones. A similar pattern of abundance was observed for Verrucumicrobia, which was prevalent only in MCZ (Fig. 1).
Bacilli and Alphaproteobacteria were the most dominant class among the four contrasting climatic zones, followed by Actinobacteria, Planctomycetia, Clostridia and Thermoleophilia. In MCZ, the class level bacterial community composition varied from the rest of the zones as Alphaproteobacteria, Betaproteobacteria, Planctomycetia, and Phycisphaerae were considerably high in MCZ, whereas, Bacilli, Actinobacteria, and Deltaproteobacteria were less compared to other zones (Additional file 6). Similarly, at the order level, the predominance of Bacillales was observed in TWCZ, ACZ, and HSCZ compared to MCZ, where Rhizobiales showed more predominance (Additional file 7). In family level distribution, Bacillaceae was predominant in all the zones except MCZ, where Gemmataceae, Hyphomicrobiaceae, Gaiellaceae, Bradyrhizobiaceae were predominant over Bacillaceae (Additional file 8). Further at the genus level, Bacillus was the most dominant genus in TWCZ (31%), ACZ (30%), and HSCZ (31%). In contrast, Bradyrhizobium was the most dominant genus in MCZ (8%), but a noteworthy proportion of the bacterial population remained unclassified as the genera were not assigned any nomenclature (novel genus). The pattern of the most abundant genera was different in MCZ compared to the other zones. The genus Paenibacillus was among the top 10 genera in all the zones except MCZ. The genera Chthoniobacter and Mycobacterium were only observed in MCZ as the top abundant ones compared to the other zones (Fig. 2). A significant share of bacterial communities present in the climatic zones was not identifiable at the species level and categorized as an unidentified bacterium. Bacillus megaterium, Bacillus pumilis and Bacillus subtilis were present among the top 10 abundant species in TWCZ, ACZ and HSCZ. In contrast, Bradyrhizobium spp. showed high prevalence in MCZ compared to the other three zones (Fig. 3). Shared bacterial community abundance was also assessed by plotting a Venn diagram, which showed a total of 18.1% bacterial community shared among all the climatic zones. Maximum shared community abundance (4.8%) was observed between HSCZ and MCZ, whereas a minimum abundance (1.2%) was observed between TWCZ and ACZ. The distribution of unique species (not shared among the climatic zones) in the different climatic zones varied, and it was found more (16.5%) in TWCZ, with a little less (11.4%) in HSCZ and almost equally distributed (4.9%) between ACZ and MCZ (Fig. 4). In conclusion, Bacillus emerged as a prominent genus of native soil bacterial community in all the zones except in MCZ, where Bradyrhizobium was the most dominant.