Pepper plant got droopy, leaning over. Stem is a bit mushy

Hi Lynee, thanks for your reply, first time poster here....
the key here is that I did NOT plant from seed.  I brought some small plants from outside that were not doing well in soil, thought I'd give them a chance in an aero and just see what happens, they were likely going to die outside.  This was a first time experiment, based on seeing people grow roots from cuttings just by leaving cuttings in water.  They almost all grew GREAT!  and most went back outside into soil. 
I kept this one in the aero.
My "mistake" was that I put the original stem all (or almost) the way down the length of the grow sponge, with some roots sticking out the bottom.  So for many weeks, was growing both plant and roots robustly, but the original stem was slowly rotting inside the grow sponge.  I pulled it apart and it was a shriveled, brown, skinny stem.  So, recently, it must've stopped passing water up the plant.  
The others that I took back outside only had their stems submerged for a short time while they thrived in the aero (roots and plant look great), and I planted them outside, they seem to be doing amazing now.   The just didn't have time to rot. 
But this one had stem under water much longer, and was rotting.  After I posted, I went to pull the pod out to inspect the roots, and the plant just fell off.  However, roots look super healthy. 
LESSON LEARNED: do not submerge the stem.  I needed to somehow only put roots in the sponge, if I put a seedling/starter in a sponge (or maybe just a bit of stem). For a small plant, this should work and stand up on its own. 

to be complete: white stuff is the dried end of a cut stem, slightly out of focus.
Yes to AG pods and sponges.
Yes only filling to the fill line.  

pardon the lengthy answer, but wanted to get it all down in case anyone else has similar issue, as I could not find any info online similar to this.  

All the best, happy growing!

Hi Shawn, thanks for sharing your experience.  
the stem was in great health when I started it.  As you described, it sat water logged for way too long, and degraded, which I described in my reply to Lynnee. 
I chopped off the bad part, put the plant in a glass of water and it perked up overnight.
I'm guessing all the flower buds will drop?  But at least I know the main plant seemed healthy, and it was not some other problem.  Who knows, maybe it will root, keep a bud or two. 
And YES, I will be going through my first winter with aero's, looking forward to it.
After I figure out these plants, looking forward to planting from seed. 
Happy Growing and good luck with your tree!

banjo, it does sound like you figured out the problem! Stems definitely don't like being submerged in water, or in soil. When you transplant seedlings, you always want to place the base of the stems at the level of the soil in your pot, so that only the roots are actually in the soil.

I've never tried to transplant something from soil to a hydroponic system--what an interesting experiment! Did you rinse the roots first, to get the soil off?

I wonder whether you could do a successful transplant to a Kratky setup? Kratkys require you to leave an air space below the plant Itself, for the "air roots"--only the ends of the long roots are actually submerged in water. There is a lot of information on Kratkys in the "Kratky System" section of this forum.



EDIT: I forgot about strawberry crowns. Those definitely start their lives in soil, and they grow reasonably well in AGs if you keep the pH right and do frequent R&Rs. So I have tried a soil-to-AG transplant, sort of!

Ha! I didn't know that pepper and tomato plants will put out roots from the stem if planted deep in soil, banjo!