Endophytes (literally “inside plants”) were first found in 1809 by examining plant sections under the microscope. They are fungal, or bacterial, or viral inclusions in plant tissues – 'foreign' materials, found in very large numbers. They're permanent fixtures, being transmitted from generation to generation of plants either through the seeds, propagation, or by ‘infection’.

In the few plant types which have had their endophyte populations closely examined, it's not uncommon to find hundreds of different species - especially fungi.

It was originally thought that they were parasitic, but over the years it was discovered that they almost always appear to have have some kind of beneficial effect on the 'host' plant, and were therefore re-classed as symbiotic.

Almost every plant so far examined has endophytes of some type. They are so widespread that the current view is that the endophytes and plants have a so-called ‘pair-wise’ relationship – with the ‘host’ and endophytes living as a mutually beneficial paired system.

For the most part, the relationship with the ‘host’ plant, and any two-way beneficial system exchanges are unknown.

“All plants, including crop species, harbor a community of fungal endophyte species, yet we know little about the biotic factors that are important in endophyte community assembly.
[…]
We now know that plants host a diversity of microbes. This is a paradigm shift away from conceptualizing plants as organisms beset by herbivores and pathogens – or engaged only in two-way mutualisms. We are now beginning to consider how the in planta microbial community figures into pair-wise models of host and pathogen.”

Source (technical details) : Evolutionary Applications, 3(5-6): 525–537.

Note : In a recent twist to the endophyte puzzle, it has been discovered that some plants can include man-made nano-plastic particles into their structure. Examples have been studied in lab. experiments, and have also been found in specimens of wild-growing plants. The mechanisms for this are poorly understood - as are the implications. Example studies : [1] , [2]

Also see : Stromulesplugin-autotooltip__plain plugin-autotooltip_bigStromules

"A stromule is a microscopic structure found in plant cells. Stromules (stroma-filled tubules) are highly dynamic structures extending from the surface of all plastid types, including proplastids, chloroplasts, etioplasts, leucoplasts, amyloplasts, and chromoplasts."

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