Not the author of this paper but am current PhD student focused on viroid discovery. There's no TEM but there are good methods such as RNAfold [0] for predicting their structures. In the case of rod-shaped RNAs, the prediction methods are quite good since it basically comes down to looking for substrings of reverse complement sequences within the circular RNA.

[0]: http://dx.doi.org/10.1186/1748-7188-6-26

The actual item is required to understand where it occurs and if these sequences have other explanations.

Considering it's predicted shape is that of obelisk ("rod") one is left to imagine that this finding has only metagenomics behind it.