We too often struggle to find nodules, even on putatively N-fixing species. Sometimes they are there, sometimes not, and almost always very small. We developed a new protocol for estimating symbiotic N fixation that may be helpful. Sullivan et al. 2014 in PNAS-USA. you should find a PDF on my RG profile.
Two answers so far; both very useful. I have had a first read of Sullivan et al. Thank you for that very interesting information. Awaiting more answers.
Dipjyoti Chakraborty, thank you for the suggestion. Which leguminous tree species did you succeed in seeing nodules by your suggested method? We have been trying it, but so far without success.