If you are not familiar with tomato plants, bumps on the stem (especially near the base) are normal. These bumps will grow roots if they come in contact with soil. But at the same time tomato plants are very susceptible to getting stem rot if conditions are continuously too moist at the base of the plant. I'm not sure how big the plants were when you changed over from using straight water, to using nutrients.

But considering that for three fourths of the plants life they had no access to the necessary nutrients, I suspect the chlorosis is likely due to nutrient deficiency from the beginning of the plants life. Assuming that you only started using nutrients in the last week as mentioned. Signs of nutrient deficiency and toxicity take time to develop, So signs of them are often noticed only after a nutrient change. Leading people to think it was something that was different after the change, rather than something from before the change. Especially with elements like calcium that are not mobile in the plant tissue. Once those plant cells developed, the damage cant be un-done by simply supplying more calcium. Although the new growth would be normal.

Thanks for the reply, homehydro. I see what you mean about the bumps on the stem now. A few of the bumps closer to the top of the rapid rooter have grown fat white roots that are already hanging into the nutrient solution. These new roots that are obviously a much whiter mass than the old slightly brown roots. The old roots aren't brown enough to indicate a large presence of Pythium, just a slight tint compared to these new roots which are bright white. The newest set of leaves that just opened today look fairly healthy. I might just trim some of the worst of the old leaves and hopefully it stays healthy from now on. Did you see the pictures? Have you ever seen rotten bumps on the leaves like that before? Is there still any possibility of it being a virus? I read somewhere that if the midrib and veins on the underside of the leaf blade are purple then that indicates a virus. Some leaves on my plant have purple veins. I suppose I'll start germinating another few tomato seeds then just in case.

Purple in the veins can also indicate a nutrient deficiency. Phosphorus, I believe.
I agree with homehydro's wait and see approach. might as well cut the bad leaves too as they're just sapping the plant of energy.

Jesse_83
Ya, I did see the pictures. I can post a bunch of links to sites that show pictures of tomato plant problems, as well as give descriptions of each nutrient deficiency and/or toxicity. Although I think that probably only be confusing and possibly even just serve to scare you. Like I mentioned Calcium is not a mobile element (nutrient) in plant tissue. It helps forms the cell walls, acting like a glue that holds all the cells together. When the cells form without the needed calcium, they are damaged cells. They begin to break down and/or decompose, causing all sorts of symptoms that can look like just about anything. That can even cause secondary infections of the plant, because of the rotting plant tissue. Bottom line is that unless you really know what your doing, telling if something was caused by a calcium deficiency is very hard to do. As far as I can tell, having the plant tissue tested is the only sure way to tell.

There is always a possibility of a virus, fungal disease, pathogens, pests etc. affecting the plants. Like I mentioned especially if they are suffering from a nutrient deficiency and their being a secondary infection. Even pests like aphids can transmit viruses to your plants. Even high humidity and/or leaves that remain wet can cause fungal diseases. Bottom line is that tomato plants are very susceptible to problems (even without nutrient problems).

But if it were me, I would mix the nutrient solution to the recommend strength for heavy growth for now. Give them at about two weeks to recover, then re-asses the situation. If they recover, then probably drop it back to about 75% to 90% recommend strength for heavy growth. I might even start some new seeds, if the first plants recover, then stick the new ones outside in the ground somewhere.

I just thought I would add a link to an article that helps explain what I am talking about in regards to calcium deficiency's. But as grizz summed up from my original post, I would wait and see if the plants recover from being deprived of nutrients before making any hasty decisions. This just gives some incite as how extensive problems from one nutrient can be.

Calcium: A Transportation Problem

Thank you all for the informative replies! Homehydro, as you mentioned there are many web sites with pictures of specific nutrient deficiencies for tomato plants, unfortunately I have not been able to find any pictures showing combinations of certain deficiencies or, as in my case, total nutrient deficiency.

I have since stopped at the hydro store and picked up a bottle of SuperThrive and a bag of hydroton. Per recommendation of my local hydro store employee, I have covered the top of the perlite with a mound of hydroton. This serves to keep light off of the rapid rooter and perlite which were developing algae colonies. I changed the nutrient solution and added 3/4 strength 3-2-6 liquid nutrients as well as a drop of the SuperThrive.

Also on your advice, I trimmed any leaves that showed signs of malformation. New vegetative growth so far looks healthy and green, and new leaves are continuing development. I know that my nutrient solution is probably a little warm because the ambient temp is around 88 degrees. This is probably causing the browning of the roots (pythium?) correct? I am still seeing new white fat roots coming out of the basket, but it seems like they only last a day or two then they join the browned mass of old roots. I think the plant would be doing better if I kept the solution cooler, because it wouldn't be expending so much energy trying to establish a solid root system.

I'm going to read up more on nutrients, which seem to be the most complicated part of hydroponic gardening. Well, maybe aside from heat management that is. Is there any reasonable way to keep the root mass bright white and healthy instead of turning brown?

Tomato new growth and roots:

http://i662.photobucket.com/albums/uu342/henleyphotography/Tomato%20Plant%20Problems/P1050317.jpg

http://i662.photobucket.com/albums/uu342/henleyphotography/Tomato%20Plant%20Problems/P1050316.jpg

http://i662.photobucket.com/albums/uu342/henleyphotography/Tomato%20Plant%20Problems/P1050319.jpg

Pepper seedling and roots:

http://i662.photobucket.com/albums/uu342/henleyphotography/Tomato%20Plant%20Problems/P1050320.jpg

http://i662.photobucket.com/albums/uu342/henleyphotography/Tomato%20Plant%20Problems/P1050321.jpg

Those are not the worst looking roots in the world. They're brown but not dead. that could simply be algae living on the roots. your plants are still very young. don't be surprised at the new root growth. at full size, a tomato's roots will probably fill 1/4=1/3 of a 5 gallon bucket.
I think your plants are fine. you've bumped up the nutrient levels, so give it some time to see the effect.

One caveat; it appears the net pot contacts the nutrient solution. you might want to lower the nute level so its 1/2"-1" lower than the net pot. you might be keeping the root mass concealed in the perlite excessively wet.

A tip for keeping you nutrient cool presented, I believe, by Joe is to simply freeze some plain water in a plastic bottle then put it in the solution to cool it down. the mass of frozen water will take a while to melt and since it's capped, won't dilute the nutes. keep two in the freezer and you can rotate them daily. Also, 88° isn't unbearable for most plants so don't try to bring them down to 60° or something.

Jesse_83
"Homehydro, as you mentioned there are many web sites with pictures of specific nutrient deficiencies for tomato plants, unfortunately I have not been able to find any pictures showing combination's of certain deficiencies or, as in my case, total nutrient deficiency.".

That's the exact reason that I didn't want to post them/any in this case. Because most people spend so much time convinced that there is a problem, and trying to compare pictures and descriptions in order to find one. As an example, if you have a blemish on your skin and were determined to find the cause. The first thing that resembled what you saw, you would likely just assume that was exactly it, (just because it was the first thing you saw). Even if there were hundreds of other similar symptoms that could causes the exact same thing, or had symptoms that excluded it from being the problem.

Most people just assume that the first one they can compare to is the problem without doing more research.. That's the main reason I brought up calcium deficiency's in the first place. Simply because they can resemble just about any deficiency and/or toxicity, (and sometimes disease). SO PICTURES WONT REALLY HELP, when one problem can look like all the others, (& visa versa). I know that is hard to understand (I have been there myself), but the more you look into it the more you understand it.

Don't get me wrong, I'm not wanting to deprive anyone from any information. And if you still want me to I will post all the links that I can think of that might be related to tomato and nutrient deficiency as well as diseases. I am not going to re-read them to point out possible problem areas for plants where I don't have first had experience with, or even knowledge of all the details. So I leave that up to the grower to decide what apply's to their situation.

But I have been in that exact same situation before myself (looking for the exact picture of what my tomato plants looked like), as well as the symptoms. I spent months searching for it and without plant tissue testing there was no real way to say exactly. Most people think there is only one cause, but there can be multiple factors for the plants problems, and after months of talking to people at General Hydroponics as well as searching for pictures and descriptions for diseases from good sources. I concluded that there were multiple factors in my plants problems.

I still got nice tomato's off of them. The way i have learned to approach it, is by eliminating all the factors that I can, then give time to re-assess the situation. Then I will send e-mails to the nutrient manufacture (with pictures) for ideas (what's there to loose there). Bottom line from sending out feelers, and assessing the feedback,. I generally get what I need to know.

If I remember correctly you said that you think your nutrient solution is on the warm side, but I don't remember seeing any numbers. I think grizz made a reference to about 88A (if that's 88F degrees Fahrenheit), that's too high in my book, just on the verge of pointless destruction. And would be a definite cause of browning (cooking) roots. Another cause for browning roots is the nutrients themselves. Tinting the new white roots is normal. Though not usually with roots that new, but all nutrients are different in that department.

Bottom line I would still be in the wait and see mode, it has only been a couple of days scene you upped the nuts. You need to give it time to make a conclusion before you make another change, or you will never know witch change made the difference and/or how much.

Jesse_83
what's going on with the plants now?