Author Topic: Tomato Microbiome article  (Read 1120 times)

William S.

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Tomato Microbiome article
« on: 2019-12-08, 06:35:37 AM »
Western Montana garden, glacial lake Missoula sediment lacustrian silty clay mollisoil sometimes with added sand in places. Zone 6A with 100 to 130 frost free days

Ferdzy

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Re: Tomato Microbiome article
« Reply #1 on: 2019-12-08, 07:32:14 AM »
Interesting.

I can see this going in 2 directions: possibly in a few years we will be able to buy "tomato inoculant" the same way we can buy "bean inoculant".

The other is that we may change our ways of saving seeds. When I'm lazy rather than put them through the fermentation process, I give them a quick rinse and let them dry on paper towel. Maybe it's better to not even rinse them?

And in the end my garden is soooo full of septoria leaf spot fungus that I will probably just have to keep on with my current method of dealing with it: very rampant, indeterminate tomato varieties only.

Woody Gardener

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Re: Tomato Microbiome article
« Reply #2 on: 2019-12-08, 10:11:53 AM »
https://www.sciencedaily.com/releases/2019/12/191206100139.htm

So we can cultivate tomato microbiomes.

Fascinating article, thanks William.

I've noticed that volunteer tomatoes tend to be more robust and to fruit earlier  than my carefully saved seeds that were fermented before drying. I think I'll do a little experimenting next year with fallen tomatoes; moving them to a row and leaving some whole and some crushed.

Steph S

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Re: Tomato Microbiome article
« Reply #3 on: 2019-12-08, 01:17:52 PM »
It is interesting.   I would have like to see their method of inoculation - how they first collect and then spray the microbiome on the plants.
Full text link is there but $10 to see it..  not bad compared to some but for a budget of zero it's over limit.

This makes me stop and think about the selection process for disease resistance in tomatoes.   I've been working with some sibling lines that have excellent foliage health (with a few exceptions that of course get culled).  I had no time for them this year and didn't need it - no disease issues.  The fruit  also have great shelf life and keeping qualities.   I started extremely late this year so had a load of green fruit to harvest.   Cut off day for tomatoes was the end of October, everything ripened off the vine except for a few gooseberry or smaller sized fruit, and I haven't seen one moldy fruit.  Those that are past the end of ripe are just wrinkling and drying out on the plate.  And they're sweet and tasty, a zero loss harvest.  This is definitely where I want to be with my tomato breeding project. 
But this raises a whole other question - how much of this effect can be attributed to the plant genetics, and how much to microbiome?   And another question I guess, if leaves have a microbiome, do fruit then also benefit from the same microbiome?

I've read some work on the root microbiome around seed germination, and seemed that it is way out of control, inoculation-wise.  The micro community changes dramatically during the germination and sprouting process.   Dowsing with beneficials did not produce any survivors in the work I read.

William S.

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Re: Tomato Microbiome article
« Reply #4 on: 2019-12-08, 03:05:53 PM »
Potentially complex interactions between genome, epigenome, and microbiome. We may already be selecting for genetics that interact well with microbiome.
« Last Edit: 2019-12-08, 04:11:15 PM by William S. »
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Joseph Lofthouse

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Re: Tomato Microbiome article
« Reply #5 on: 2019-12-08, 05:47:55 PM »
I have often wondered if I should be including soil samples from my garden when I share seeds.  Or if I aught to inoculate tomato seeds with soil from my tomato patch before sharing.

gmuller

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Re: Tomato Microbiome article
« Reply #6 on: 2019-12-09, 01:12:50 PM »
This is a great eye opener for me - how come I didn't think about this before? Let me digress. A few years ago, I was looking for a yoghurt culture that would not go all ropey and weird after a few generations ( like commercial cultures do). I wanted a self sustaining yoghurt starter that I could keep using over and over. One solution I came across - start yoghurt with the stems of chilli fruits. Works a treat. My starter culture is is fantastic.
Extrapolating on this - I wonder if the dilute milk spray that is recommended for powdery mildew on cucurbits is a way of promoting/feeding leaf microbiome? Sort of yoghurt in reverse.
Ditto folar sprays of seaweed solution.
G

gmuller

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Re: Tomato Microbiome article
« Reply #7 on: 2019-12-09, 01:27:05 PM »
It is interesting.   I would have like to see their method of inoculation - how they first collect and then spray the microbiome on the plants.
.
From the paper
" Above-ground plant material was collected
from various genotypes of tomatoes across 9 different sites spread through 4
fields. Plant material was submerged in sterile phosphate freezing buffer and
sonicated for 10 min in a Branson M5800 sonicating water bath. The resulting
leaf wash from each site was pooled and divided into 6 aliquots and stored in
glycerol freezing buffer. For each inoculation in the 1st passage, an aliquot
was thawed, and cells were pelleted and resuspended in 200 mL of 10 mM
MgCl2 buffer. Of this, 40 mL was heat-killed in an autoclave for a 30 min at
121 C. Both live and heat-killed inoculum was plated. There was no growth
from heat-killed inoculum, and the live-inoculum concentration was calculated to be 1.1 106 colony-forming units/mL. Soil from each site, which had
been stored at −20 C, was combined in a sterile bucket and thoroughly
mixed before inoculation.
Inoculation Procedure.
Soil inoculation. The top layer of every pot was supplemented with 40 g of UC
Davis Farm Soil. Soil inoculation was only performed once and only for the 1st
passage of plants.
Spray inoculation. Each plant was sprayed with 4.5 mL of inocula using misting
spray tops. Control plants from passage 1 were inoculated with the heatkilled inocula. Control plants from P2 onward were inoculated with sterile
10 mM MgCl2. Immediately after inoculation, plants were placed in a random order in a high-humidity misting chamber for 24 h. After 24 h, the
plants were moved to a greenhouse bench. Plants were inoculated once per
week in the same manner and were placed in the misting chamber for 24 h
after every inoculation."

GM

Joseph Lofthouse

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Re: Tomato Microbiome article
« Reply #8 on: 2019-12-09, 01:55:59 PM »

Hmm. Solanum pennellii only grows well for me in one particular batch of compost. I wonder if that has more to do with the microbes in that batch than with the mineral/organic composition?

Steph S

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Re: Tomato Microbiome article
« Reply #9 on: 2019-12-09, 03:22:45 PM »
GM, thank you for sharing the details.   :)

Lactobacillus spp are indeed widely associated with seeds and multiply during the germination stage.  When we ferment tomato pulp to clean the seeds, the lactobacillus required for the process is already present on the fruit.   So it makes perfect sense that chili stems would have some inoculum for your yoghurt.  8)

The Lactobacillus crew in general have some helpful antipathogenic effects.  For example:
In spring wheat, activity reported against Fusarium and Alternaria
https://www.tandfonline.com/doi/abs/10.1080/09583157.2014.964661
In alfalfa silage, activity reported against Clostridium, Listeria, Salmonella, E coli.
https://scielo.conicyt.cl/scielo.php?script=sci_arttext&pid=S0718-58392015000400005

Some spp have been reported in the leaf microbiome but not in great numbers in the one paper I saw just now.  They would be at their best where there's a chance to go anaerobic and ferment something of course.   They have to hang around the fruit to get onto the seeds I guess for a whirl around the germination cycle.  :D  Maybe milk treatments are helpful because they artificially increase the population in a place they are not usually dominant, but are still having beneficial effects against pathogens.  Milk gives them something good to grow in.

Steph S

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Re: Tomato Microbiome article
« Reply #10 on: 2019-12-09, 04:29:39 PM »
Hmm. Solanum pennellii only grows well for me in one particular batch of compost. I wonder if that has more to do with the microbes in that batch than with the mineral/organic composition?

Different plant species might have some difference in the root secretions that nourish the community they need to survive.   Maybe that compost has the right match of microbes that are happy with the pennelii root sugars.

I sometimes wonder about my home garden compost - why is it  better than anything else - even the high quality organic compost that I buy from a local supplier.    Is it the trace minerals, from bits of clay on the roots of the weeds tossed in?  Is it the broken bits of eggshells that provide a special surface something good likes to grow?    Is the particle size a bit coarser and is that why it retains moisture better?   Maybe it is because the compost microbiome is  adapted to my site environment?   Don't know why, but for some reason everything likes the home stuff best.  Mostly made of weeds... ???

William S.

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Re: Tomato Microbiome article
« Reply #11 on: 2019-12-09, 04:30:47 PM »
Pink Pigmented Methylotrophs can be important. A graduate student I knew once did a study on them. Apparently with ecological restoration using glyphosate they get knocked out. Innoculation helps with recovery of the pink pigment methylotrophs and possibly the plant communities.

Easy to work with in culture, colonies are pink on agar.

https://en.m.wikipedia.org/wiki/Pink-Pigmented_Facultative_Methylotrophs
Western Montana garden, glacial lake Missoula sediment lacustrian silty clay mollisoil sometimes with added sand in places. Zone 6A with 100 to 130 frost free days

reed

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Re: Tomato Microbiome article
« Reply #12 on: 2019-12-10, 08:53:47 AM »
Pink pigmented, does it mean that literally? I ask cause I see what I suppose is a particular fungus in my garden all the time. It's kind of stringy, for lack of better word with lots of branching.  I see it in composting material and when I hoe or dig in the soil. It is generally white but I have seen pink coloring and sometimes yellow. Often it runs in a line along a decaying stem or up and down the inside of a tunnel left by a worm or decayed root.
« Last Edit: 2019-12-10, 08:56:04 AM by reed »

William S.

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Re: Tomato Microbiome article
« Reply #13 on: 2019-12-10, 09:15:48 AM »
Yes, but only shows up in agar. I think pink stuff you are seeing is perhaps fungal. Though not certain.
Western Montana garden, glacial lake Missoula sediment lacustrian silty clay mollisoil sometimes with added sand in places. Zone 6A with 100 to 130 frost free days

reed

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Re: Tomato Microbiome article
« Reply #14 on: 2019-12-10, 09:52:48 AM »
Yea, I'm sure it's a fungus and like I said generally white but sometimes areas will have a slight pink tint.  I see yellow less often but it is much more prominent, like it is maybe a different but possibly associated organism cause don't usually see it by itself. Don't matter all that much I don't reckon, organic matter is getting turned back into soil and my vegetables seem to like it.