Rhizosphere is the region which is biologically active and enriched with microbes. The chemical, biological and physical characteristics of this area have great significance on the plant roots. We noticed that rhizosphere region has significant effect on soil physico-chemical properties and rhizospheric bacterial dynamicity and diversity. Previous study shown that soil bacterial communities have great contribution in nutrient cycling. Carbon metabolites secreted by plant roots promote growth and activities of microbes inhabited in the soil surrounding the roots (Hussain et al. 2011). Parallelly rhizosphere microbes benefit plants by supplying nutrient and growth stimulating hormones phytopathogen and enhancing tolerance to environmental stress (Mendes et al. 2013). Physical and chemical properties indicate the health of the agricultural soil. Soil collected from the RRS and PRS indicates slight alkaline in nature due to prevalence of the soil belt in the intertidal region of Sundarbans, India, but the soil samples from RRN and PRN are neutral. The experimental results are in good agreement with previously published results observed by different researcher (Ghosh et al. 2019; Karak et al. 2013; Ponnamperuma 1972). The high conductivity, organic carbon content and fair distribution of the metals like Ca, Na, Mg and K for the entire soil sample gives us insight into the availability of the essential nutrient in the rhizosphere environment which helps in proliferation of microbial population in this area (Karak et al. 2013). The salinity of the PRS and RRS was found to be higher than PRN and RRN, which indicates the presence of the soluble salt which essentially increases the conductivity of the soil. Clay content for all the soil was found to be higher with respect to the coarse sand, fine sand and silt that in turn might also provide better condition for the microbial growth in the rhizospheric region (Biesgen et al. 2020).
The distribution of the metal content in the soil considerably varies as per the sampling locations. Few factors like- (a) soil characteristics like grain size of the soil, organic carbon content, Mn or Fe oxygenated hydroxides, chelating agent as well as ligands (Banerjee et al 2012); (b) substrate variation due to natural weathering of the soil (Zhang and Gao 2015); and (c) discharge of pollutions and anthropogenic pressure determines the distribution of the elements in the soil (Ghosh et al. 2020). The gradient of distribution of elements indicates presence of high concentration of Fe and Al which generally occurs due to natural weathering or due to presence of basaltic and lateritic rocks present in the soil (Nath et al. 2013). The enrich prevalence of heavy metals like Cd, Co, Cr, Cu, Ni, Pb and Zn might occur due to natural factors or anthropogenic pressure like uneven use of pesticides, insecticides, and chemical fertilizers (Ghosh et al. 2019). The level of K might occur due to presence of granodiorites and granites in the soil (Ghosh et al. 2019). High occurrence of Fe might occur due to hydrological fluctuation e.g., alternate period of wet and dry season in the crop cultivated agricultural land (Dohrmann et al. 2013).
In our study, we have found total 29 phyla, 85 classes, 315 families and 639 genera from the tested samples (Table S8-S11). The total OTUs of four different samples of PRN, PRS, RRN and RRS are 7353, 7172, 9038 and 6391, respectively. Rhizospheric bacterial alpha-diversity were higher in both monocot and dicot grown in normal soil than the saline soil. Beta-diversity shows random distribution of bacterial population in all the four samples. We have identified total 29 phyla in all four samples. Among them Actinobacteria, Acidobacteria, Chloroflexi, Cyanobacteria, Firmicutes, Gemmatimonadetes, and Proteobacteria were higher in abundance than other 22 phylum. Previous research has shown that Proteobacteria, Acidobacteria, Actinobacteria, Bacteroidetes and Firmicutes were dominant phyla in the rhizosphere soil of Arabidopsis and cotton (Lundberg et al. 2012; Qiao et al. 2017). Total 85 bacterial classes were identified across four samples. Actinobacteria, Acidobacteria, Acidobacteria, Thermoleophilia, Anaerolineae, Chloroflexia, Bacilli, Clostridia, Gemmatimonadetes, Alpha-proteobacteria, Betaproteobacteria, Deltaproteobacteria, Gamm-aproteobacteria were the higher relative abundance classes in four sampling sites. Different species of Actinobacteria were responsible for recycling of nutrient in a great extent of rhizosphere soil (Bhattacharyya et al. 2016; Connon and Giovannoni 2002; Handelsman 2004) and this Actinobacteria is the most abundant phylum in the rhizospheric soil PRN, PRS and RRN. However, the rhizospheric soil of RRS showed Acidobacteria as most abundant but they have quite high abundance of Actinobacteria as well. Previous study showed that Acidobacteria could grow in environment which is nutrient less and also showing higher abundance in poor soil (Zou et al. 2005). Acidobacteria and Actinobacteria were found to be abundant in disease-suppressive soils and reported to be responsible to suppress disease-causing microbes and trigger enhancement of beneficial microbes that have potential to promote crop health (Sanguin et al. 2009). Pseudonocardiaceae is the most dominant families in the sample PRN whereas Nocardioidaceae (33.99%) in PRS relative abundance. Actinomycetales is the most dominant in the RRN but Acidobacteria in the RRS sample. The relative abundances of the bacterial communities at the genus level in four rhizospheric soil were significantly different. Although Actinopolysporaceae group of genera was the most dominant bacteria in the sample PRN. Nocardioides was the enriched bacteria in the sample PRS. Telmatobactor was the most dominant genus in the sample RRS. Proteobacteria, Acidobacteria, Actinobacteria, Firmicutes and Planctomycetes were most dominant bacteria among all bacterial community found in the rice rhizosphere soil (Bhattacharyya et al. 2016). The Proteobacteria, Acidobacteria, Actinobacteria, Chloroflexi and Firmicutes are dominant taxonomic group in most of the soil samples. Actinobacteria and proteobacteria has also been reported dominant taxonomic group found in rhizospheres soil of Maize (Dohrmann et al. 2013). Decomposition of organic matter are performed by the Chloroflexi. PGPR activity like siderophore production, IAA production, nitrogen fixation and prevention of different phytopathogen are fascinated by the group of Firmicutes and Proteobacteria (Felestrino et al. 2017; v et al. 2005).
Analysis of the rhizospheric microbiome of peanut grown in normal and saline soil delineates that the Acetobacteraceae, Bacillaceae, Gaiellaceae, Gemmatimonadaceae, Micromonosporaceae, Mycobacteriaceae, Pseudonocardiaceae, Solirubrobacteraceae, Sphingomonadaceae, Thermomonosporaceae, Xanthomonadaceae are the most dominant family in PRN. And among these, Xanthomonadaceae shows higher fold shift in PRN than PRS whereas Anaerolineaceae, Chloroflexi, Nocardioidaceae are found to be the dominant family in PRS than in PRN. The genus of Actinocorallia, Hydrogenedens, Kaistia, Kibdelosporangium, Koribacter, Marmoricola, Nakamurella, Nitriliruptor, Plantactinospora, Prauserella, Pseudonocardiaceae, Solirubrobacterales, Sphingomonas, Sphingopyxis, Stella, Xanthomonadales were higher abundant in normal soil in respect to saline soil, as well as Bellilinea, Chloroflexaceae, Longilinea, Nocardioides, Nocardiopsis, Pelolinea were dominant genus in saline soil in compare to normal soil. Similarly, rhizospheric microbiome of rice between normal and saline soil condition, the families Chloroflexi, Nocardioidaceae, Solirubrobacteraceae, Streptomycetaceae, Thermoleophilaceae, Thermomonosporaceae were dominant fold increase values in normal rhizospheric soil than the saline condition, whereas Acetobacter and Gematimonadaceae were the highest fold increase in saline rhizosphere soil compare to normal soil. The genus Actinocorallia, Aminicenantes, Chloroflexaceae, Marmoricola, Nocardioides, Nocardiopsis, Plantactinospora, Prauserella, Solirubrobacterales, Streptomycetaceae, Thermoleophilum, were the higher fold increase in normal rhizosphere than saline soil. Hydrogenedens, Koribacter, Paludibaculum, Telmatobacter were showed a higher fold increase in saline rhizosphere than the normal soil. Several studies reported Sphingomonadaceae, Chitinophagaceae, Nocardioidaceae, Solibacteraceae, Bacillaceace, Cytophagaceae and Methylobacteriaceae were predominant families (> 2% relative abundance) of T. aestivum L rhizosphere region and different bacterial genera like Sphingomonas, Microvirga, Bacillus, Nocardioides, Marmoricola, Bryobacter, Flavisolibacter were the dominant (> 1% relative abundance) (Rousk et al. 2010; Latif et al. 2020). Whereas Bacillus nealsonii, Rhodospirillales_bacterium_WX36 and Bacillus niacini were prominent (> 0.5% relative abundance) bacterial species (Latif et al. 2020). Sphingomonas, Kaistia, Xanthomonadales were unique genus belong to phylum Proteobacteria and Nakamurella, Plantactinospora, Thermomonospora, from Actinobacteria; genus Stella from Bacteroidetes present only in the rhizosphere of PRN, whereas genus Pelolinea, Longilinea belong to phylum Chloroflexi were found only in PRS. It was interesting that phylum Chloroflexi has been found only in the rhizosphere of PRS. Similarly, the genus Thermoleophilum, Prausere, Solirubrobacterales, Rhodococcus, Marmoricola from phylum Actinobacteria; Methyloceanibacter, Rhodospirillales from Proteobacteria and Aminicenantes has been found distinctively only in the rhizosphere RRN, whereas genus Paludibaculum, Koribacter from Acidobacteria were found only in the rhizosphere of RRS.
The influence of different environmental factors describing the microbial community is like the finding of beta diversity analysis due to differences of rhizospheric community to the monocot and dicot types (Fig. 7). Factors corresponding to the differences in the bacterial communities were pH, EC, Salinity, Coarse Sand, Al, Cd, Cr, Fe, Ni. Pb and K along with the first axis explaining 69.2% and the second axis (28.57%) of the variation (Fig. 8). CCA plot shows that pH, EC, Salinity, Coarse Sand, Al, Cr, Fe, Ni. Pb were the most important environmental factors to significantly influence the rhizosphere bacterial phylum abundance (Fig. 8). Previous study has shown bacterial community structure were influenced by pH, Cr, Sb, As, Zn and moisture content, but pH was the most dominant factor (Guo et al. 2019).
The clustering of PCoA and CCA analysis signify PRN and RRN were clustered into the same group, while PRS and RRS were situated distantly. The CCA result in our study indicate pH, EC, Salinity, Coarse Sand, Al, Cr, Fe, Ni. Pb is positively correlated with rhizospheric community structure. Thus, pH, EC, Salinity, Coarse Sand, Al, Cr, Fe, Ni. Pb appeared to be an important factor that influence microbial communities and dynamics.