**4. Conclusions**

Biological control provides an alternative for chemical fertilizers and reduces costs as well as environmental pollution. *Trichoderma* spp. are a good source of secondary metabolites. Co-cultivation of these beneficial fungi can stimulate the synthesis of novel secondary metabolites better than in monocultures. These *Trichoderma* cultures in combination can be used in field trials as they are able to inhibit the growth of the *Xanthomonas oryzae* pv. *oryzae* in in vitro conditions. The maximum zone of inhibition was recorded from the co-cultures rather than the monocultures. Biosynthesized ZnO NPs were also able to inhibit the growth of the *Xanthomonas oryzae* pv. *oryzae* in in vitro conditions, which was found to be dose-dependent.

**Supplementary Materials:** The following are available online at http://www.mdpi.com/2309-608X/6/3/181/ s1, Figure S1. Screening of fungal discs (*Trichoderma* spp.) for antibacterial activity against *Xanthomonas oryzae* pv. *oryzae* A- MBXoo69, B- MBXoo53 (+- tetracycline - distilled water). Figure S2: Antibacterial activity of zinc oxide nanoparticles (ZnO NPs) against *Xanthomonas oryzae* pv. *oryzae*(Xoo) by disc diffusion method (+ ve = tetracycline; − ve = distilled water). Figure S3: Bacterial sensitivity test of biosynthesized zinc oxide nanoparticles from *Trichoderma harzianum* (PGT4) (MH429899.1), *Trichoderma reesei* (PGT5) (MH429901.1), *Trichoderma reesei* (PGT13) (MH429900.1) and co-culture of *Trichoderma* sp. (PGTA) against different strains of plant pathogen *Xanthomonas oryzae* pv. *oryzae* (MF579736.1) (concentration in µg/ml) (a- Trail 1, b- Trail 2, and c- Trail 3). Table S1: Place of collection of infected samples from different crop-growing regions of Karnataka. Table S2: Places of Rhizospheric soil sample collection. Table S3: Morphological and physiology characters of Rhizosphere Trichoderma spp. fungi.

**Author Contributions:** Conceptualization, T.R.L. and S.C.; Data curation, M.A.A. (Mohammad Azam Ansari), A.A., M.A.A. (Mohammad A. Alzohairy), S.B., R.A. and S.R.N.; Formal analysis, T.R.L., A.A., M.A.A. (Mohammad A. Alzohairy) and S.R.N.; Investigation, B.S. and S.B.; Methodology, B.S.; Resources, T.R.L., M.A.A. (Mohammad Azam Ansari), A.A., M.A.A. (Mohammad A. Alzohairy), S.B. and R.A.; Software, M.A.A. (Mohammad Azam Ansari) and M.A.A. (Mohammad A. Alzohairy); Supervision, S.C.; Visualization, S.B.; Writing—original draft, B.S. and T.R.L.; Writing—review and editing, M.A.A. (Mohammad Azam Ansari), R.A., S.R.N. and S.C. All authors have read and agreed to the published version of the manuscript.

**Funding:** This research was funded by UGC SAP-DRS II program and University Grants Commission (UGC)-New Delhi, India for providing financial support under UGC Rajiv Gandhi National Fellowship for SC (No. 201516-RGNF-2015-17-SC-KAR-19382).

**Conflicts of Interest:** The authors declare no conflict of interest. The funders had no role in the design of the study; in the collection, analyses, or interpretation of data; in the writing of the manuscript, or in the decision to publish the results.
