Both of your reasoning are correct. What you have to do is define your definition of endophyte and proceed.

You can even do both I would say. If your analysis is based on amplicons, you can pool everything and sequence.

Thank you for your reply.

By 'amplicons' you mean targeted amplicon sequencing (using 16S or ITS)?

Regarding the definition of endophytes, why are mycorrhizae and rhizobia usually not included under endophytes?

Yes, amplicon means any marker gene amplicons, it can be 16S or any other marker.

With definition, I mean definition in your context, that if you want to see the endophytes when you grow hydroponically or in soil.

I never meant that you change the definition of endophyte all together. And I can't really understand why are you comparing mycorrhiza and Rhizobia.

Mycorrhiza is not an organism and Rhizobium is endophyte, or rhizobium is most common endophyte what generally people know about.

You need to read some articles regarding how and what you want to analyse. There are many endophytes which can grow and live well in soil. So, you need to think before you make your experimental design.

Thanks.... I meant mycorrhizal fungi only.... Are they also considered to be endophytes?

You need to look into the classification of mycorrhiza. There are two classes: endo- and ecto-mycorrhiza.

Hello Dr. Mishra.

First a general comment on your question:

The endophytic community will certainly be distinguished in plants grown in the soil and in a hydroponic system. Considering a purely endophytic community is something that can be achieved with the germination of seeds in a sterile chamber. In this condition, the seedling will have a native endophytic community. It is worth noting that the development of plants is closely related to their microbiome, and must count endophytic, epiphytic microorganisms (rhizosphere, phylloplane, bulk soil) and their interactions with plant species.

Therefore, evaluating the endophytic community requires both microorganisms from the seed itself and all other microorganisms capable of colonizing the newly germinated plant endophytically.

Answer:

If financial resources are available, the metagenome of endophytes associated with cultivation in soil and hydroponics could reveal important results regarding not only the structure and composition of the community, but also reveal the functional role, so perhaps you could think about management strategies in both systems to guarantee increased production and quality of the plant species of interest.

Thank you very much for your reply.

Could you share some protocols for evaluating the endophytic microbiome under sterile conditions as well as for growing the plants hydroponically.