Something eating my bean seeds?

Hello everyone,

My family has been growing all kinds of beans for decades (even generations) without any significant issue. This year however, we're having some major issues.
We have a couple hundred square meters of bean rows we grow, and out of that we got a near 0 "germination rate" (quoted because it's not an accurate term in this case). The seeds themselves are fine - as in, they sprout just fine when testing (even when we eat them, we always sprout them and they sprout just fine) however there must be something eating them underground. I tried digging around looking for them and could barely find any, and the few I found did actually sprout, but had their stem chewed off before it managed to get out of the soil and had lots of wormholes and even worms (or some kind of larvae?) in the actual seed - these "worms" are completely white and quite small (multiple fit in a single bean seed). The few that actually managed to get their stem out of the soil are clearly chewed as well (even the leaves).

Due to this (chewed leaves) I initially thought that we had bird issues where they were eating the leaves (which we dealt with in the past), but seeing the "germination rate" + the seeds themselves are nowhere to be found underground (for the most part) that's to rule out. I don't believe this can be a  "ground animal" causing this (e.g. birds, chipmunks, ...). This is also not a mouse/rat since there are no holes or tunnels underground.
What really baffles me is the degree of the damage (it's thousands of plants/seeds we're talking about) and I find it hard to believe that we have enough "worms" in our garden to wipe out this many. Also because when digging around, other than a couple of worms in a single bean seed, I couldn't find any at all. (and again, this issue is completely foreign to us, we grew beans and other crops in that location just fine in the past, and didn't do anything different than usual - as in amendments, etc - this year)

If anyone has any insight in regards to this I'd really appreciate it, thanks 🙏

Maybe you have cut worms?

https://permies.com/t/136860/Permaculture-controls-cutworms

Hey Anne,

Honestly I doubt. Definitely not what I saw inside of that one bean. Also, I don't think I've ever seen those around here.

Did you have some sort of worm in the seed?  If you are starting over might try freezing the seed for 48+ hours before planting in case there is something inside them.

My thoughts lean to birds or rodents.

I don't grow beans in such a large area, or with the same long term experience of your family, but the last two years I did have poor success with growing beans due to both these pests.  The fact that the beans seem to have disappeared completely suggests this to me. This year has been fine for me though, with few losses, maybe I'm starting to get a balance, maybe it's just been a lucky year for me... The beans I grow are fava beans, they often carry bean weevils which leave holes in the seeds, but don't usually affect the germination.
However, mice and birds often leave tell tale evidence at the surface of their digging for the beans and it seems you have seen no evidence of that.

Looking for differences to previous years:
Any difference in the seed source - Do you save your own seed?
Any difference in weather patterns: temperature, watering/rainfall?
Have you lost a cat or other higher predator that might affect pests like birds and rodents?
Any other crops affected?
Any pattern in the beans that survive?

Can you describe the worms and the damaged seedlings more? Maybe a picture? I'm wondering if they are a result or the cause of the problem.

C. Letellier wrote:Did you have some sort of worm in the seed?  If you are starting over might try freezing the seed for 48+ hours before planting in case there is something inside them.

Hey, the seeds are most definitely fine. I mean... we eat them all the time, and we also always sprout them before eating, and they sprout just fine.

Nancy Reading wrote:My thoughts lean to birds or rodents.

Hey Nancy,

We do save our own seeds and have always done so. Our method didn't change this year (other than maybe we used to not let the beans fully dry up on the plant before harvesting, but I doubt this has anything to do with them disappearing underground). As far as weather goes, it's not significantly different this year.
We did till and plant 1-2 weeks later than usual because we were dealing with broken equipment, and that (coupled with a very warm April) lead to the garden being quite overgrown with weeds. For context, we generally always start sowing no earlier than May due to our climate.
To re-iterate on the birds/rodents point: we did have issues with birds in the past where they were eating the leaves of the fresh sprouts (never the actual seed underground) and for that we always placed some row cover over the fresh seedlings for a couple of weeks (which we did this time as well seeing the first beans that sprouted were chewed up). Only now I found out that the reason the rest weren't sprouting was because the seeds literally weren't there anymore.
No other crops affected: we have potatoes just next by and they are coming up great, and carrots and cover crops (and some grains) further away which are also growing regularly. For the rest of the garden we don't direct seed, but the seedlings are also just fine. Other than perhaps clover (wild clover that grows as a "weed") which has its leaves chewed as well.

I did attach a few pictures below. Most of them show you how the seedlings that managed to sprout look. The first one on top (the one with the black "thing" and the blue circle) is a fava bean turned to mush basically (the seeds with worms inside are all mushy), but if you look close enough inside the blue circle, there are a couple of white spots which are the worms I'm talking about. It's definitely not super clear, but they're way too small for me to get a good picture with my camera. The last one at the bottom is a picture of a white bean where if you look close enough you'll be able to see wormholes.

Hope this helps in some way.

maybe fungus gnat larvae?

https://flourishingplants.com/white-worms-in-soil/

https://en.m.wikipedia.org/wiki/Fungus_gnat

Judith Browning wrote:maybe fungus gnat larvae?

Hey Judith, that was one of my initial guesses based on the research I did. However I'm not entirely sure that's the one because fungus gnat larvae tend to have a black head and/or some black on/in their bodies, as well as they tend to be somewhat translucent. This doesn't really align with what I'm seeing. Also, I don't see fungus gnats flying around, I maybe saw a single one this year and it wasn't near the garden (mind you, I'm outside most of the time). Given they also tend to have a very short life cycle, I'm guessing I would've seen much more flying around the garden. Also it seems that they mostly affect indoor plants?

The closest looking thing I found when researching this initially is pot worms, but reading about them it seems that people only (?) find them in their worm bins, so I'm not sure either.

I must admit I'm a bit stumped.

Drying the beans on the plant would, I would think, make them better keepers rather than not. Unless your weather is so hot as to cook the beans.

You say the ground was overrun with weeds? So when you tilled there was more organic material in the soil? That seems unlikely to be an issue, unless it was causing the bean seeds to also rot.

I'm now leaning towards the seeds not germinating for some reason and then being eaten by the worms. Usually that happens when the soil is cold and wet, but fava beans are pretty tolerant of that, so I don't think this is likely to be the problem either.

If the worms are the problem then diversity of planting, attracting predatory insects and other creatures by habitat and food sources are the usual recommendations. If you really think that the worms are going to continue to be an issue then you may be able to get some predatory nematodes to water in.

Get you a hand pump sprayer and mix up some water and strong peppermint oil solution. Spray on the ground around the plant. Plant some nasturtiums and marigolds too around the beans. You may need companion plants or mix up the plants around you.

Don't sound like you rotate your beds. Maybe the insects are gaining ground because of this. Try to rotate every seven years if possible. I know it's not practical sometimes. In nature, the animals when they poop out the seeds, do it for us.

The peppermint should will burn them up pretty good though lol

Tobacco water is also good if you don't have much solanacium growing nearby.

An update on this after more research and reflection:

I was looking into something called "damping off" disease. In short, this is either fungus or mold that cause the seeds to rot, caused by wet soil and cold temperatures. The idea of having enough pests in my garden to cause such a major issue never sat right with me. Damping off disease makes much more sense and the symptoms do line up: extremely low survival rate, seeds literally disappearing from underground, the seeds that are left are rotten/mushy, often they are also blackened, the seedlings that manage to survive have visible damage (e.g. black spots), ... (lines up with the pictures I sent as well). This would also explain why I didn't see any pest in the soil when digging around.

On second thought, I have onions planted just nearby and compared to a different patch further away in a different garden, these are slightly behind (though not by much) and have had lower survival rate (planted from bulbs). (in this case maybe a handful didn't come up, compared to the beans where a handful did come up). I did find a couple of rotten bulbs, which looked just like the rotten bean seeds I found. At this point I'm starting to believe that the worms I was seeing were just a symptom, and thinking about it, these look just like the worms I find in my chickens's manure after it's been sitting there for a bit, when it doesn't dry up well (e.g. sitting in a pile). Which would explain why during my research I haven't managed to find a pest that looked exactly like what I was seeing in my garden - because these aren't pests, they're just there to clean up/decompose.

However I still have no clue why this didn't happen in the past as well, since we had basically the same weather and planted even earlier. Perhaps I'm misremembering. Also, this garden is on a slope, so drainage is pretty good. Either way this year after planting we definitely had a bunch of rain and cold weather (a couple of frosts as well).

Now I'm still in time to replant, which is what I will do. I also came across a technique called solarization which is used as a "natural" fumigant and involves placing a transparent tarp on the soil, leave it there for a few hours up to a few weeks depending on the temperature at the time. This will amplify the heat of the sun which will warm up the soil to the point that the fungi will be killed off. I'm not sure if this is necessary in my case since the weather is quite nice right now and it's meant to stay this way for a bit, meaning the soil dried up pretty well. We're also far enough in the season where temperatures should stay warm and we shouldn't have as much rain as in the spring. Also the onions I mentioned earlier (other that the handful that rotted/disappeared) are doing fine, and I planted those maybe a week or so after the beans (which were planted all at once). Also I definitely can't leave it on for more than a few hours, maybe a couple of days at most given our growing season is short and I need to replant as soon as possible either way. If anyone has experience with this, I'd appreciate some insights. (also I'd assume this would kill off beneficials as well, so if it's unnecessary I'll happily avoid doing it).

Hopefully the next lot of beans will be fine then - please let us know.
It would be interesting to confirm whether the weather was significantly different this year at the time of planting, if you are able to look that up. Strange, I think of Italy as having long hot summers - you must be up in the hills!

I live up in the mountains actually haha. And I'm remote/rural enough to where there's no way for me to get accurate past weather data, other than logging it myself (which I didn't do sadly).

Update: after re-seeding everything is growing great. So I guess this confirms my thesis that it was just "unlucky" timing in terms of wet weather and cold temperatures. I wonder if this could've been avoided by simply having better drainage (given I've heard mixed things from people living close by, where some sowed at the same time and had the same issue while others had no issues)?

Anyways, I appreciate all the pointers I received in this forum 🙏