In the ancient agriculture practices farmers are using leguminous plants in field to enhance of soil fertility, which possess Rhizobium bacteria that has mechanism to acquire nitrogen from air to soluble form. In addition, in this research isolated strain Trichoderma longibrachiatum GFT2 act as biofertilizer and biocontrol agent which has been characterized by performing chitinase (18.56 U/ml), glucanase (13.82U/ml) and IAA production (7.3000µg/ml), PO4 solubilization (10.7142 µg/ml), siderophore production (77.5%). Root colonization assay performed for detection of Trichoderma longibrachiatum GFT2 which colonized over the root or not, further compability test isolated Rhizobium pusense PR4 and Trichoderma longibrachiatum GFT2 for capable to each other on same environment or not. Moreover, Application of Trichoderma longibrachiatum GFT2 and Rhizobium pusense PR4 on peanut plant (Arachis hypogaea) seed germination and nodule formation. Maximum seed germination rate was shown in seed treated with PR4+GFT2 (39%), whereas least number (01) of nodules formed in plant treated with dual culture Trichoderma longibrachiatum GFT2 and Rhizobium pusense PR4. Maximum Sixteen nodules formation in plant treated with in Rhizobium pusense PR4 was observed. In this paper, we analysed the how Trichoderma longibrachiatum GFT2 effected on peanut plant (Arachis hypogaea) nodulation process when applying in soil and reduced the number of nodules by indirectly inhibit or decline the growth of nodulation bacteria. We can determine the precise interaction between Trichoderma longibrachiatum GFT2 and whether their alteration of soil profiles is due to them by analysing soil samples for meta transcriptomics.