The classification suggested that 99% of the sequences belonged to Bacteria, while 0.4% belonged to Archaea (as shown in Figure 2).
In Bacterial sequences, the major three groups included Proteobacteria(44%), Terrabacteria (27%) and PVC (12%) (Planctomycetes, Verthatrucomicrobia and Chlamydiae) superphyla.
The major superphyla Proteobacteria, comprised of Delta/Epsilon Proteobacteria(17%), Alpha Proteobacteria(12%), Gamma Proteobacteria(7%) and Beta Proteobacteria (6%) in that order of abundance (Figure 3).
The majority of the sequences analyzed by all the methods, belonged to the phylum Proteobacteria, which includes a wide variety of pathogens, such as Escherichia, Salmonella, Vibrio, Helicobacter, Yersinia and many other notable genera. Others are free-living (nonparasitic), and include many of the bacteria which are responsible for nitrogen fixation.
Most abundant class of Proteobacteria in the turns out to be Alphaproteobacteria, which include agriculturally important bacteria capable of inducing nitrogen fixation in symbiosis with plants. The rhizosphere soil depicted the high abundance of nitrogen-fixing bacteria. Heliobacterium modesticaldum Ice1, was the most abundant of all the microbial community according to MEGAN analysis which is a well known nitrogen-fixing bacterium.
The sequence based phylogenetic analyses revealed further interesting results - the presence of few eukaryotic sequences including a few fungi and cyanobacteria members were identified (Figure 4).
Apart from this fragment based sequencing revealed the presence of few higher plant species such as Oryza, Medicago and Gossypium probably originating from adjoining deposition of reproductive propagules from adding cultivation fields. The bacterial phylogeny (Fig 5 A and B) revealed similar results as those obtained in the KRAKEN analyses.
All the sets which have been considered for the study reveals proteobacterial abundance.
The samples exhibit significant uniqueness in their core functions The meta network analysis reveals the major interacting genera to be Pelomonas in both the cases of the epiphytic as well as terrestrial root endophytes of the pteridophytes.
The samples revealed on an average 2% of the total abundance to be human pathogens.