Endophytes

[Joseph Lofthouse]

Endophytes, are the microbes, viruses, fungi, and bacteria that live inside plants and form mutually beneficial symbiotic relationships with the plant.

Endophyte spores are typically incorporated into the seeds by the plants, either by depositing onto the cell coat, or internally. These symbiotic relationships are millions of years old. I believe that they are vital to the health and well being of our plants and ecosystems. They provide nutrients to the plants, and protect against pathogens, and pests.

Would it be too woo-woo of me to suggest that the plants, and the symbiotic endophytes are all part of the same genome? I wonder how much of the changes that are sometimes attributed to epigenetics are actually due to endophytes?

I've been giving a lot of thought this year, to how I can more fully share the complete endophytic (and exophytic) ecosystem of my plants when I'm sharing seeds. Should I be providing samples of the soil where my tomatoes grew? Should I be spraying my bean seeds with a diluted soil extract?

I am certain that treating seeds with fungicides or other poisons is damaging the plants ability to thrive. But then I welcome even the pathogenic microbes, because they teach my plants how to survive long-term.

I'm working on building a video course that includes a chapter about endophytes in relation to landrace gardening. Can we have a discussion here about what you'd like to see in that course?



 

[Ocimum]

Interesting topic!

There is however always the threat of the pathogens, which you already mention. In some cases, introducing diseases, like Xylella fastidiosa to Europe, or the Chestnut blight to America, destroyed the livelihoods of many people. Maybe it would be best to do this soil inoculation only short distances, where pathogens anyway move?

It would be sad if the Maize Lethal Necrosis disease, https://www.youtube.com/watch?v=422DDNAlB6s which emerged in Africa and leading to hunger there, would be brought to Latin-America, where people are also dependent on this crop.
And there are many other disease which are not yet known. If there are major diseases wiping out whole crops, the biodiversity is reduced as well, threatening resilience when the next disease comes.

[Nicollas]

Carole Deppe talks about selecting for soil at the same time that she select individuals. Iirc she saves some soil, but i dont know if it is linked with the individuals or the species.

[Tim DH]

Hi Joseph,
   Interesting thoughts. ... In the vegetable patch I conduct a fairly strict rotation of crops, with the specific aim of reducing soil transfer.
I accept that is partly because rotation is what I've been taught.  But partly it is because when I have experienced problems (for example Onion White Rot or Brassica Club Root) I can trace it back to a failure in the rotation.

       On the other hand, with the orchids, I do get problems re-potting into 'new' compost. Sometimes young roots appear to be 'burnt' in the new compost and I have wondered if that is caused by the roots coming into contact with the wrong microbes because the right ones aren't there!

       Tim DH

[reed]

Interesting topic for sure. I had never heard the term before so will have to do some reading up before commenting. One question, are the bacteria that help plants form nitrogen nodules on the examples of this?

[William S.]

Very artificial human concept endophytes. The community of organisms associated with plants is only partially inside them. It is also on every surface and nearby.

I have attended a very few meetings of plant ecologists discussing just a few plant associated organisms. Just enough to know I know nothing.

Speaking of knowing nothing. Knowing next to nothing about the entire science of plant pathology has led me to an kind of easy come easy go methodology in the garden. I grow plants that grow well for me and don't bother with ones that do not.

This attitude in general has led me to abandon or pause work on small grains and quinoa. Small grains the problem is Hungarian partridge. Quinoa an unknown pathogen that does not bother orach or the weed chenopodium album.

[William S.]

Interesting topic for sure. I had never heard the term before so will have to do some reading up before commenting. One question, are the bacteria that help plants form nitrogen nodules on the examples of this?

Good question if not it is an example of the artificiality of beginning and ending a discussion of plant associated communities of organisms at some arbitrary barrier. Yes some organisms are inside plants. That is amazing! However the interactions don't stop there but continue. Are nitrogen fixation nodules that or part of the continuation? Does it even matter? Mycorhizzae are a continuation right? We can buy or attempt to buy those two classes of microbes to improve your garden. In fifty years will we be buying innoculum for additional groups?

[reed]

I'm seeing more and larger nitrogen nodules in my garden. Runner beans especially have more than I remember in the past. I think it may have something to do with introducing some new crops from heirloom and or organic sources. Specifically, cowpeas, soybeans and peanuts all of which, especially the peanuts have a lot of nodules.

I can't say for sure that is what it is, but I've even seen weird little knots of some kind on tomato roots. I don't think tomatoes do that or at least I've never heard of it but if it's a disease or parasite instead, I can't tell that from the plant's growth and production.

[William S.]

I'm seeing more and larger nitrogen nodules in my garden. Runner beans especially have more than I remember in the past. I think it may have something to do with introducing some new crops from heirloom and or organic sources. Specifically, cowpeas, soybeans and peanuts all of which, especially the peanuts have a lot of nodules.

I can't say for sure that is what it is, but I've even seen weird little knots of some kind on tomato roots. I don't think tomatoes do that or at least I've never heard of it but if it's a disease or parasite instead, I can't tell that from the plant's growth and production.

I say I know nothing about plant pathology and then in less than thirty seconds of Googling I found this for you:

https://www.growveg.com/plant-diseases/us-and-canada/tomato-root-knot-nematodes/#:~:text=Tomatoes%20are%20moderately%20susceptible%20to%20root%20knot%20nematodes.,are%20destroyed%2C%20and%20irregular%20galls%20take%20their%20place.

Increasing root nodules in legumes could be a very positive sign that your garden is very friendly towards the bacteria involved.

[Joseph Lofthouse]

Yup. Arbitrary and capricious to try to separate the symbiotic microbes that live inside the plant cells, from those that live between cells, from those that live just outside the roots, from those that live in the general vicinity.

I wonder if part of the amazing vigor of the promiscuous tomatoes, is because plants that have found beneficial microbes are able to share them more readily using bees as a vector.

[whwoz]

When research into this started, mainly to try and germinate orchid seed, which is very small, it was thought that it was only fungi working with orchids.  Now, it is considered that the only plant family that does not rely on endophytes to some extent is the Proteaceae, which have protepid roots to scavenge phosphorus doing the same task. It maybe found that even these have some other association down the track

[reed]

I say I know nothing about plant pathology and then in less than thirty seconds of Googling I found this for you:

https://www.growveg.com/plant-diseases/us-and-canada/tomato-root-knot-nematodes/#:~:text=Tomatoes%20are%20moderately%20susceptible%20to%20root%20knot%20nematodes.,are%20destroyed%2C%20and%20irregular%20galls%20take%20their%20place.

Interesting, as it sounds like the white bumps, I see on tomatoes are result a parasite and logically should be detrimental, but I don't see that in the growth and production of the plants. Only at end of season when I pull them up do I occasionally see them.

Increasing root nodules in legumes could be a very positive sign that your garden is very friendly towards the bacteria involved.

More than 50 years ago my garden was part of a tobacco patch and no doubt poisoned in the extreme. Then it was left to be part of a hay field for some years and then abandoned to locust and cedar thicket. In the last twenty plus years it has been amended with all manner of organic stuff harvested from around the place. Noting ever leaves it diseased or otherwise, except for what gets eaten. I suspect that about any local thing and maybe some imported on seed, that can live it, does live it. Seed of some crops including some of my tomatoes have been saved from it over that time as well. Maybe that is long enough for unseen relationships to have developed. 

I have always grown a lot of tomatoes but only sometimes grew winter squash and never large amounts of squash. Also, I generally did not save squash seed. Maybe that's why with increasing disease and bug issues the tomatoes still do fine but I can barely get a squash to mature at all.

Who knows? It's just one of those things I find interesting to contemplate but not enough so to go to the trouble of trying to fully understand it.

[Steph S]

Indeed it seems to me that at one time all the excitement was about VAM mycorrhizae in field crops, and endophytes were only known in Poacea crops (and orchids of course!).
This is probably the reason for drawing a line between the in vs out symbionts, since endophytes were officially "not found" in any crops except grains, until more recently proven to be wrong.

Here is a study of culturable endophytes:
https://www.nature.com/articles/s41598-018-38230-x
Notice that they carefuly sterilized the outsides of the plants to ensure that only endophytes were cultured.  They wanted to be sure the organisms they cultured were in fact endophytes.
Also the fungi were cultured on antibiotic PDA plates to prevent bacterial growth, so not a kombucha!
After isolating and growing them all up, they made a broth from spores and mycelia rinsed off the plates, and used that to inoculate the crops.
I doubt that would work as a way of distributing endophytes with your seeds, you would probably need to dry or somehow get them in a dormant condition ready to be sprouted and applied in the field.
Interesting to notice, though, that they did in fact find endophytes in seeds themselves, as well as other tissues.  So you may be distributing more than you think.

Just noting as well, this study found vastly more culturable endophytes in organic compared with conventional farms.  Obviously using fungicides and etc messes with the plant's internal microbiome as well.  Maybe some useful stats there for your course.

It is interesting that some of the isolates are recognizable to me as known pathogens of the crops.  (Fusariums, Alternaria, etc)
I wonder if they help growth in any way, or are they just lying dormant to fulfill their function of rotting it down when the time comes.
I've given this a lot of thought regarding tomatoes, I do believe that hosting rots is adaptive, to get their seeds out of the wet gel and into some condition to survive winter by drying out first.   I'm selecting them to be more dependent on the animal in attendance (me).

As for the woo-woo, well you and I and every other living thing are all part of the same diversified genome, everything alive on this planet has some DNA in common, and it stands to reason that different organisms work together for common cause.  But I think it would be just confusing the issue, to say that the endophytes and plants are 'the same genome'.  The endophytes aren't found in the plant's DNA - they have their own DNA kept separately, and just happen to live inside the plants.   

Viruses OTOH are something else, but I believe the relationship (including in some cases, a presence in our DNA) is very very far from being understood. I wouldn't consider them in the same package as endophytes. 

[gmuller]

Drifting slightly away from the strictly endophyte topic.
Thinking like a plant for a moment - do we need to do anything apart from encourage natural processes?
Fermenting tomato seeds seems to make sense in terms of natural recruitment strategies the plants might have.
But what other dispersal mechanisms are at play?
Wind dispersed seed might be highly adaptable to widely dispersed microbiota, since they are likely to end up elsewhere than on the parental soil. What can we surmise from animal dispersed seeds, or water dispersed propagules?
How does a bean or pea naturally disperse? should some pod material be included in distributed seed?
How does refrigeration affect seed biomes? What might be the repercussions for material accessed from seed banks where i imagine sterility is a high priority? (This has got me thinking about the seedbank landraces I accessed for my fava grex from widely dispersed global seedbanks and markets.) Does the flotation method I use to clean allium seed wash away important biome material?
What are the ethical questions (alluded to above) where we distribute biome-rich propagules but also include pathogens to naïve gardeners (and gardens) who might not welcome Joseph's 'pests as selection filters' approach, but instead suffer crop failure?
This has got me thinking.

[Joseph Lofthouse]

Every fall, I get inquiries from people that are along the lines of "How do I Keep Powdery Mildew from Killing my Squash". I'm like, "Powdery mildew didn't kill your squash. Fall killed your squash. The powdery mildew just bloomed after the squash had already finished it's life cycle".