Finally-- some research that ties together microbes + genetics, and our two courses.
How have I missed this for the last three years!
It’s yet another argument against heirlooms and variety isolation in general. And it explains why the trichoderma experiment in tomatoes benefitted the wild types more than the domestic types.
Actually it explains so much.
If you are like me this research will be like a
((This research found that soil microbes significantly influence “hybrid vigor,” in corn. Experiments showed that microbes in the soil have a greater impact on the growth and health of hybrid corn plants compared to inbred ones. ))
True, how much better would it be with better soil practices. This research said that in sterile soil, inbred corn and hybrid corn performed the same, what’s there is apparently alive enough to give hybrid corn the advantage.
But that’s not what I see as the biggest issue that we can actually do something to affect. It’s all the small farmers and gardeners spending tons of time, money, energy and resources on improving soil, only to plant plants that cannot associate with the existing soil life.
This is an interesting idea. In my garden pathways between beds, I let weeds have their day for a few months last year. I pulled out grass and obnoxious weeds, leaving the good weeds that I approved of.
It turns out the process was highly inefficient. I perhaps was benefiting the soil, but the time to observe and analyze each individual weed was just too long and tedious. To make matters worse, my favorite weed which is a low ground crawler with easy pull roots, appears to have went to seed and donated them all over my pathways.
I decided to just hoe the pathways indiscriminately. Now it’s just cold dirt out there that’s not threatening to take over. It’s amazing how efficient a simple oscillating hoe is at solving my weed problems. In a matter of minutes, I can destroy hundreds of competitors and then call it a day.
I have a reasonable size backyard garden. My point is it’s tough to effectively help the corn out without buying inputs. My goals are to develop crops and methodologies that produce a lot of food under very low or zero purchases outside of buying seeds.
Yes, thanks Julia for sharing. It is a good argument against inbreeding and its consequences in terms of ability to deal and work with microbial communities, i.e. with the soil…
I would love to read the same study with hybrids vs really heterogenous populations… I believe that it is where the difference will be even more relevant to our practises, as no farmer cultivates inbred corn, i.e. homozygous.
On a side note, some may find interesting this overall debunking of the overall “heterosis” paradigm, which is some produce of junk science, or mystification Jean-Pierre Berlan, From a Mercenary to an Emancipated Agronomy, 2011 – Et vous n’avez encore rien vu… and the “Hybrids or Heterozygous Clones?” paragraph.
To summarize it: in recent times, with corn (outcrossing, heterozygous), breeders make inbred lines (homozygous, and kind of “stupid” in the field, to say the least, so to say always sick, and not yielding) then they cross them intentionnally, doing heterozygous F1 (“clones” or “quasi-clones”), so it grows much better, and call that “the mystery of heterosis”… And start monopolozing by, factually, just selecting within the initial genetic variability -the same as the wheat breeders did before, with a mostly inbreeding crop, initially grown in populations, i.e. landraces, from which they first took “pure lines” prior to do directed crosses, which at each stage made yield gains -. And so nothing mysterious, just directed crosses within the “genepool”. And it has been a century students have been taught to think in that paradigm, with this so called “mystery” at the center, which does not help… There is not such a thing as “heterosis” in normal outcrossing populations, as there cannot be inbred lines.
It is a side note, but as their experience is all in this biased ideology/paradigm, that is why I say it would be even more relevant for us to have a comparison between f1 hybrids and diverse corn populations in relation with soil organisms.
From this podcast discussion, practical steps a farmer can take include:
Consider Soil Microbes: Acknowledge the role of soil microbes in influencing hybrid vigor in crops, particularly maize. Understanding the interaction between crops and local microbial communities can be valuable.
Experiment with Microbial Communities: Explore the impact of different microbial communities on plant growth. Conduct experiments in controlled environments, such as gnotobiotic growth systems, to observe how plants respond to varying microbial conditions.
Optimize Planting Practices: Depending on the findings, farmers may need to optimize their planting practices. For instance, if certain microbial strains negatively affect inbred lines, strategies to mitigate these effects might be considered.
Explore Soil Sterilization Techniques: Understand the implications of soil sterilization on hybrid vigor. Experiment with different soil sterilization techniques to observe how they affect crop growth and heterosis.
Collaborate and Stay Informed: Engage with researchers and stay informed about advancements in understanding hybrid vigor and its molecular mechanisms. Collaboration between researchers, farmers, and policymakers can contribute to sustainable agriculture practices.
Adapt Farming Practices: Depending on the specific findings, farmers may need to adapt their farming practices to harness the benefits of hybrid vigor without encountering negative microbial influences.
Contribute to Future Research: Support or participate in ongoing research to further unravel the molecular-level mechanisms behind hybrid vigor. Contributing to this knowledge base can lead to more informed and sustainable agricultural practices in the future.
Podcast Interview: Maggie Wagner and Manuel Kleiner
PNAS: Welcome to Science Sessions, the podcast of the Proceedings of the National
Academy of Sciences, where we connect you with Academy members, researchers,
and policymakers. Join us as we explore the stories behind the science. I’m Taylor
Gedeon, and I’m speaking with Maggie Wagner of the University of Kansas and Manuel
Kleiner of North Carolina State University. In a recent PNAS article, Wagner, Kleiner,
and colleagues report that the interaction between maize and soil microbes influences
hybrid vigor, or heterosis. However, mixed results from further experimentation suggest
that the composition of the microbial community may be an important factor. PNAS
caught up with Wagner and Kleiner on the implications of their findings.
Maggie, what is hybrid vigor, and what role does it play in commercial farming?
Wagner: Hybrid vigor refers to this phenomenon, which is really common among a lot
of different plant species, and particularly crop species where, when you crossbreed
between two inbred lines of a plant, their offspring are much more vigorous, healthier,
more productive than either of the two parents.
Most commercial corn production is using just hybrids. And so when you look out at a
cornfield, most of those plants will be hybrids, and probably the exact same hybrid
between the two parents. The use of hybrid cultivars for commercial agriculture was one
of the most important innovations in agriculture in the early- to mid-20th century. Making
this transition to using hybrids has been responsible for a lot of the huge increases in
grain production that we’ve seen over the last century.
PNAS: Why did you focus on the potential role of local microbial communities in the
hybrid vigor of maize?
Wagner: For a while my research has been focused on looking at how plants with
different genotypes interact differently with microbes, and specifically how plants with
different genotypes will form microbiomes that differ from each other. One of the
experiments that I ran when I was a postdoc at North Carolina State involved comparing
hybrids and inbreds and comparing the composition of their root and leaf microbiomes.
And we did find that, in the field, the composition of their rhizosphere microbiomes in
particular, which is the soil immediately surrounding their roots, differed quite a lot
between inbreds and hybrids. So when we set up that experiment, we were going to just
compare how those seven bacterial strains colonized the inbreds and hybrids in
possibly different ways. And we were assuming that the hybrid vigor of the phenotype
would still be there; we assumed that that was just inherent to the genotypes that we
were using. And so it was really surprising when we measured the biomass of these
plants just to use as a covariate in our statistical models, and, to our surprise, we did not
see the hybrid vigor up for root size in our sterile controls. That was kind of an accident,
but it sort of launched this whole project.
PNAS: Manuel, how did you compare the growth of inbred maize lines and their hybrid?
Kleiner: A lot of our experiments really rely on being able to grow plants with and
without microbes. That is really critical to understand the interactions between microbes
and plants. We need to grow systems where we can actually remove all the microbes,
and that’s what we call the gnotobiotic growth system. And so what that system really is,
it’s basically a large plastic bag that is clear. And it’s fully sterile; we buy those plastic
bags already fully sterilized—I think they are gamma irradiated to kill everything inside.
And then we take corn seeds, and we sterilize these corn seeds by applying a pretty
harsh treatment of bleach and ethanol and different things to really try to remove all the
microbes from the surface. And then we add a sterilized grow substrate; we just use a
calcinated clay which is basically just the same powdery substance that people use for
baseball diamonds. We autoclave it; we kill everything; we add that in there; the plant
has kind of a substrate to grow in; and we add our sterile seed. And then, depending on
what treatment we want to apply, we apply the microbes by watering with a solution that
has nutrients, like a plant fertilizer solution with the microbes of choice added to it.
PNAS: In your paper you highlighted seven microbial strains used in the bacterial
treatments. How did you determine this simplified synthetic microbiome for conducting
your analysis?
Kleiner: Ultimately, we actually ended up using different types of things in our growth
system. Maggie, for example, came up with the idea to later use soil slurries, where she
extracted microbes from a natural soil and added them to the bags. But the original
seven came actually from a laboratory in Harvard from Roberto Kolter’s lab. There’s
another PNAS paper on that, actually, from 2017, where they had gone through an
extensive process of trying to identify a simplified, fully defined community for corn
roots, that is corn-root associated. They tried to find which microbes are present in the
corn that they grow, and which are most representative of the community in terms of
taxonomic diversity and abundances that we find by growing corn and things like that.
PNAS: Was there a difference in the inbred and hybrid lines when grown in sterile
versus bacterial-treated soil?
Wagner: Specifically, we saw that the hybrid lines didn’t really care whether they were
in sterile conditions or in the presence of bacteria, but we saw that the inbred lines did
worse when they had these seven bacterial strains in the soil with them. That difference
in the inbred versus hybrid response to these microbial communities is what drove that
difference in hybrid vigor between those two treatments. And so that was interesting,
too: We didn’t see the hybrid getting some sort of boost from the bacteria. Instead, what
we saw was a negative effect of the bacteria, but only on the inbreds.
Immediately one thing that we thought of that could explain this, that possibly the
hybrids have a much better immune system, and maybe these bacteria are sort of
weakly pathogenic to the corn and that could explain the pattern we were seeing. But
it’s not the only explanation. It’s also possible that these bacteria are actually harmless,
but maybe the inbreds think that they’re dangerous. If the inbreds have sort of a
hyperresponsive immune system and start to defend themselves against these
harmless bacteria, that comes with a cost. It requires energy from the plant to do that,
which could result in less growth in the presence of live microbes. There’s even more
possible explanations. For example, the relative ability of the inbreds and hybrids to
compete for nutrients in the soil with those microbes and things like that.
PNAS: To determine whether natural, complex soil microbial communities also induce
heterosis, you conducted a second growth-chamber experiment and two further field
experiments in North Carolina and Kansas. What did you find?
Wagner: The gnotobiotic growth system that Manuel was describing earlier is really an
extremely simplified system that bears not much resemblance to the types of microbial
communities that these plants are experiencing when they’re actually on the farm. We
did a series of experiments of increasing complexity to try to get closer and closer to
those realistic conditions that the plants are dealing with on the farm because we
wanted to know if what we were seeing was just a fluke related to these seven bacterial
strains and really simplified conditions, or is this something more general that actually is
happening on the farm as well. First, we kept it in the lab, but we added a full soil
community, which is a whole lot more than seven bacterial strains. And we found the
same thing. And then we took it to the field. We actually used a couple different
methods to sterilize soil right there on the farm, and then grow the corn in the sterilized
soil or in a control treatment, and we saw a similar pattern in North Carolina. We did
something similar in the field in Kansas and we found that those treatments did affect
heterosis, but the story got a lot more complicated at that point because the direction of
the effect was opposite, where we actually saw heterosis, or hybrid vigor, getting
stronger after soil sterilization.
Kleiner: You have to sterilize the soil to a certain depth, and we did steaming as one
treatment. And then another one was a chemical treatment and [an] ultimate
combination of chemical treatment with a steaming treatment. And for the steaming
treatment, you have to imagine you have to have this giant steam generator that you
have to probe with a tractor or something that generates the steam, and then the steam
gets pushed through hoses into little nozzles that you stick into the field. And basically,
then you pump steam into the field for a while to really kind of heat the soil to kill
everything.
PNAS: What are the implications of these findings for future research and sustainable
agriculture?
Wagner: I think we’re still pretty far off from any direct application of this. I think the
significance of our paper is that it’s the first time anyone’s reported that just soil
microbes are involved in the expression of hybrid vigor. And we have to figure out
what’s the best way to leverage that. And to do that, we need to understand it a lot
better. We have plans to follow up on all of this and figure out how it works from the
molecular level all the way up to testing whether this happens in many different hybrids
or just some and also to try to understand which microbes are responsible for this and
how that works.
We’ve known about hybrid vigor for a very long time, but we still don’t really understand
very well how it works at the genetic level. So we’re excited about this project, in part
because of the potential applications for agriculture, but also, we’re hoping that this is
going to provide some clues for folks, not just us but in other labs, to follow up with so
that we can understand hybrid vigor a little bit better. Ideally, maybe sometime in the
future, if we can figure out how to get high-performing plants at the level of current
modern hybrids, without having to go through the process of hybridizing every single
year to produce the seed that gets planted; that would be hugely beneficial for
agriculture in general.
PNAS: Thanks for tuning into Science Sessions. You can subscribe to Science
Sessions on iTunes, Stitcher, Spotify, or wherever you get your podcasts. If you liked
this episode, please consider leaving a review and helping us spread the word. Join us
next time as we continue to explore the stories behind the science.
I totally agree with this sentiment. There is some intangible “it-ness” in any particular patch of soil which drives which plants thrive in it or sputter out. Whatever combination of factors determine it, I don’t care to know. The biological component of it can sometimes slowly shift over time, either from great effort (physically removing a dominant species over many years) or through the natural accumulated efforts of plants growing there. Different strains of the same species often behave very differently, with no obvious pattern or reason.
Luckily it isn’t all that difficult or costly to spend a season or two doing variety trials to find what works. Beyond that you can try breeding different strains to generate more diversity to sift through. Whatever “it” is in the soil is quite happy to know its own preferences.
Im intrigued, wouldn’t multiple samples of soil be considered, like wild soil that had never been farmed, just to compare results…instead of steamed and sterile…good grief good colonies of microbes have been erased from most soil amendment equations for so many years…im so happy to add wild soils to my garden, from old growth forest leaf litter. To me I would prefer to study whats alive and how these soils influence growth and yeild…but still save seeds, look at the seeds and seed coat…isn’t that where microbes sit and wait for the water, temperature, pH and day lenghth to help a sprout thrive? The seed as we know has so much growing information, genes, endophytes, even insect eggs or larva…the seeds’ ability to protect the germ inside, and the germ outside that protective barrier to the soil.
The celery patch is emerging yet on its third year…after going to seed, collecting seeds, and most falling onto the ground…getting daily waterings, going through extreme heat, 117 degrees and hotter, baking in the sun…these seeds still allow sprouts to emerge, with all of that weather and temperature bombardment…the symbiotic relationship and transition from seed to seedling, in soil that’s alive…thats were I’d put my observations.
Ask the seed what it wants, wish they could speak. I wish I were a seed whisperer, oh the stories!! I would like to attach one of those little cameras that can pass through a digestive system…to a seed, and collect data on the journey after a seed is injested, then deposited on the ground, where the seed can be left to grow. Imagine the pH changes, moisture, temperature fluctuations, bile, digestive fluids…and carried from one local to another.
