Species Diversity

[ednaknightlora]

For those naysayers who insist you must have to test for species diversiy using DNA analysis can anyone tell me of studies looking at biomass as an indicator of species diversity? I believe Dr. Elaine mentioned something about this. Thanks! Me may the microbes be ever in your favor.
Edna

[jamesdpinner]

I'm not sure what your thinking of in regards to what Dr. Ingham said. DNA analysis is precise way to test for species diversity. The qualitative assessment we use at the  Rodale Institute measures diversity by morphology, the study of shape or form, this gives us a good idea of diversity. I don't know how biomass could be used as an indicator for species diversity thats not something I'm familiar with. For stewardship of the land we simply want to know that we are supporting a diversity of species. Knowing the exact number of is unnecessary and expensive. Life in the soil is fun to learn about, but don't forget that species diversity is important above ground as well. Greg Judy is a person worthy of looking into. He does mob grazing and has been quite successful at it. He says for every species he creates a home for 10 other species follow. Bill Mollison says " you don't have a grasshopper problem you have a duck deficiency". Ok perhaps I'm getting a bit off topic. I love your enthusiasm Edna. Keep it up. And may the the microbes be with all of us!!

[Jonathan Pineault]

Hello group!

first I must say thank to Elaine for that incredible workshop about life in the soil and microscopy! Thanks to the folks at Rodale, James, Richard, Elsa... It was an awesome, most instructive week with you all and its keeps me going I this fucked up and destructive world :)

So, here in Quebec, ramial wood chip is well know because some searchers made studies about ramial wood chip restoring fungal communities and biomass in the soil. Basically, it is a waste from pruning trees for power lines or the wood industry. Go check that study : REGENERATING SOILS WITH RAMIAL CHIPPED WOOD.

We use it a lot for mulch on our clients project.

The thing is, when we do a pile of it, strictly conifer or strictly deciduous, there is a burst of actinobacterias. After one week in pile it makes tons of strands, clearly not fungi.

Check out these photos :

http://www.flickr.com/photos/ecomestible/8194489165/in/photostream
http://www.flickr.com/photos/ecomestible/8194488147/in/photostream
http://www.flickr.com/photos/ecomestible/8195579330/in/photostream
http://www.flickr.com/photos/ecomestible/8195578410/in/photostream
http://www.flickr.com/photos/ecomestible/8194485267/in/photostream
http://www.flickr.com/photos/ecomestible/8195576492/in/photostream

Elaine was talking that actinobacterias could be an indicator of going anaerobic in the pile. But for that example, the pile seem to remain aerobic. In fact, it's not really wet.

I read on wikipedia that actinobacterias are a good decomposer of cellulose and lignin.

Alex and I wondered if these actinobacterias on ramial wood chip could be suppressive of mychorizal fungi? Or are they doing the first job on cellulose and lignin so the fungi can take on? If we apply that ramial wood chip with a lot of actinobacterias on the soil, will it switch the balance of the soil in favor of bacterias instead of fungi?

What is sure is that it doesn't seem anaerobic, no smellies, no black layer, no heating over 45 Celcius.

I'm so excited about all that new stuff, few other questions will follow.

Seeking your comments on that one,


Jonathan
permaculture designer
écomestible
Quebec

[Jonathan Pineault]

Hello again everyone!

new questions.

Elaine told us during the class, that it was a really bad indicator if we saw any Vibrio (comma shaped) or Spirilla (wave shaped) bacterias.

I took few pictures and videos from my microscope wondering if our compost, which is not finished yet, was complitely lost.

Have a look at theses videos :

https://www.youtube.com/watch?v=0tpozk5RlVA
https://www.youtube.com/watch?v=pgZgmBnGQYM
https://www.youtube.com/watch?v=43G38wI8Yvo
https://www.youtube.com/watch?v=NwLwgMbJfgc
https://www.youtube.com/watch?v=c27G7KZwEzY

Especially look at the last one, the quality is better.

What are these? I can see lot of these. What does that means?


Jonathan
permaculture designer
écomestible
Québec

[Jonathan Pineault]

So last question for today,

I am making my few first qualitative assessments of microbiology in few different material. Lots of fun things to watch! Cute little flagellates...

During my assessment of our unfinished, fungal dominated compost, I saw a ciliate or two in a slide. It must be the cut grass that stays in layers and develop anaerobic conditions.

While completing the spreadsheet (in attachment), I saw that seeing 2 ciliates in 2 fields of view, gave me a number of 36 000 ciliates/ml. The standard deviation is 0.31, which is three times the number.

Because there is such a deviation, should I consider that ciliates are not a problem? Are they negligible? Is that because of the anaerobic microsites and those anaerobic conditions will be overran by the good guys (there is a lot of flagellates and amoebea)?

Help me not wondering about the future of my compost ;P 

Jonathan
permaculture designer
écomestible
Québec

PS: I give you in attachment my compost spreadsheet. It's an alpha version, so it will keep improving! You can help me to improve that tool, too!

[Edna Lora]

Hi Jonathon.

Thanks for sharing that paper and all your great photos and questions. I can't wait to See the replies. I have been making drawings of the organisms I can't identify and at this stage I'm afraid I can't identify way more than I can identify. My notebook is getting well used. 

In Georgia trees go down all the time and we can get wood chips delivered free. The chips that would otherwise go to the landfill are the tops and branches of the trees. Tree removal companies generally sell the trunks. Most of the year we will have green leaves in the mix (apparently not as good).

I usually leave the material piled up until I need it as the piles are huge and I'm sure not going to turn them. the compost piles are big enough to turn. Actinobacteria is normally present in the piles but what I see looks more powdery than your photos. The paper suggests spreading the chips right away which is interesting because I assumed mulching with fresh wood chips ties up nitrogen. 

I have been using the material as a mulch but thought I could use it to help a client reestablish grass in an approximately 1/8 acre dirt paddock without spending loads of money bringing in commercial compost. 

I recommended to her to get as much organic matter onto one of her paddock as she can this autumn. We would chip up fallen branches and trees on her property and basically create a lasagna compost, layers of carbon and layers of horse manure/hay/grass clippings, etc. I suppose this would be "composting in place".  The plus is she would be using waste material on her farm and it would be cheap. 

This paper has me reconsidering this approach so I am interested in what Elaine has to say. It would be a heck of a lot easier to just spread the wood chips in a less than 2" layer wait until spring then sow a legume. 

Thoughts?

Sent from my iPad

--
 
 

[Ingham, Elaine]

My thoughts would be to safeguard yourself from the possible pathogens ---- like the disease organism that killed the tree --- by letting that wood sit in the pile for at least a year before using,

OR

apply SEVERAL applications of good biology using a DOCUMENTED compost extract or compost tea or even an light application of good compost in order to make certain those organisms that will attack, consume, and inhibit the pathogens will be present in the organic matter when you spread it out.


Elaine R. Ingham
Chief Scientist
Rodale Institute

--

[Ingham, Elaine]

I checked out the pictures Jonathan sent. Thank you for the great shots, Jonathan!

But, see all that fuzzy wuzzy stuff? That's fungus.

The ashy, white, dry stuff is actinobacteria.

See that last shot where the fuzz is holding all that clump of wood chip together? That is fungus. I'd love to have you send me some of that to take pictures of the kind of fungus it is.

Or do you have a microscope you can pull some of that fuzzy wuzzy white stuff and get it in water and look at it with the microscope? then we could tell if it was excellent fungus, ok fungus, or worrisome fungus.

See where it might be useful to be wetting the material with a good compost extract as you are chipping it up? We could get better biology started on this material right from the beginning!

Elaine R. Ingham
Chief Scientist
Rodale Institute





-----Original Message-----

From: Jonathan Pineault [mailto:jona...@ecomestible.com]
Sent: Sun 11/18/2012 12:38 AM
To: lifein...@googlegroups.com
Subject: Actinobacteria in ramial wood chip

Hello group!

first I must say thank to Elaine for that incredible workshop about life
in the soil and microscopy! Thanks to the folks at Rodale, James,
Richard, Elsa... It was an awesome, most instructive week with you all
and its keeps me going I this fucked up and destructive world :)

So, here in Quebec, ramial wood chip is well know because some searchers
made studies about ramial wood chip restoring fungal communities and
biomass in the soil. Basically, it is a waste from pruning trees for
power lines or the wood industry. Go check that study :REGENERATING
SOILS WITH RAMIAL CHIPPED WOOD

<http://www.dirtdoctor.com/view_org_research.php?id=69>.

écomestible <http://ecomestible.com>
Quebec

--

[Ingham, Elaine]

I have been looking at the videos, and I'm not seeing anything of concern.

You had a rod shape bacterium in the first video in the list that was wiggling around a bit, but my interpretation is that it was stuck on something. It was thrashing about trying to get un-stuck, but that doesn't make is a spirillum.

Both spirilla and vibrio should be self-propelled, so when you see them, they should be moving, at least some of the time, AGAINST the flow of the water. There was a reasonable flow of water in the videos, so everything was moving. But if the only movement is with hte flow of the water, then that's not real motility. Certainly you had a tumbling bacterium, but not something I would convince myself was truly motile, and in a corkscrew or worm-like or snake-like motion.

The big round object I think you were asking about in one of the videos is most likely a ciliate cyst. Fairly clear, large, single wall, circular..... most likely a ciliate cyst.

Elaine R. Ingham
Chief Scientist
Rodale Institute





-----Original Message-----
From: Jonathan Pineault [mailto:jona...@ecomestible.com]

écomestible <http://ecomestible.com>
Québec

--

[Ingham, Elaine]

I think you nailed it exactly.

Seeing a couple ciliates in 20 fields is probably a result of the mats of organic matter not getting broken up, so you have a bit more diversity of the not-so-wonderful in your material.

Take home message: Break up those mats when you are turning.

You are interpreting the Standard deviation as compared to the mean values exactly correctly.

When the standard deviation is larger than the mean value, it means (ah, English is such a contextural language) that there is no significant difference from zero. Thus, you have representatives of the organism group present, but they are not in high enough number to get all excited about.

Problem is, the fungal data can lead you to exactly the same conclusion.

When the mean for the fungi is less than the standard deviation for fungal strands, it means you don't have a really good set of fungi in the pile.

Remember to look at diameter and color of the fungi....... are they beneficial fungi, or bad guys, most likely?

Elaine R. Ingham
Chief Scientist
Rodale Institute





-----Original Message-----
From: Jonathan Pineault [mailto:jona...@ecomestible.com]

Sent: Sun 11/18/2012 1:43 AM
To: lifein...@googlegroups.com
Subject: Unfinished compost and anaerobic condition in sections of the compost

So last question for today,

I am making my few first qualitative assessments of microbiology in few
different material. Lots of fun things to watch! Cute little flagellates...

During my assessment of our unfinished, fungal dominated compost, I saw
a ciliate or two in a slide. It must be the cut grass that stays in
layers and develop anaerobic conditions.

While completing the spreadsheet (in attachment), I saw that seeing 2
ciliates in 2 fields of view, gave me a number of 36 000 ciliates/ml.
The standard deviation is 0.31, which is three times the number.

Because there is such a deviation, should I consider that ciliates are
not a problem? Are they negligible? Is that because of the anaerobic
microsites and those anaerobic conditions will be overran by the good
guys (there is a lot of flagellates and amoebea)?

Help me not wondering about the future of my compost ;P


Jonathan
permaculture designer

écomestible <http://ecomestible.com>

Québec


PS: I give you in attachment my compost spreadsheet. It's an alpha
version, so it will keep improving! You can help me to improve that
tool, too!

--

[Jonathan Pineault]

I took samples from both piles. I'll get some shots from my microscope
and send to the list very soon. If I get to my client's house again in
the next weeks (where the photos were taken), I'll try to isolate the
white holding stuff and make some shots with my microscope, so we will
be sure to assess the right thing.

It's so awesome to be in touch with you guys!

Jonathan
permaculture designer
écomestible
Quebec

[Elsa]

Hi Jonathan,

Wow, cool pics.  I have not seen much spirila, but I did find this image which is the closest in resemblance to your spirilla video:  http://footage.shutterstock.com/clip-14734-stock-footage-educational-microscopic-rotifer-lepadella-eating-spirilla-bacteria-also-a-closeup-of-the-animal.html

In the image linked above the spirilla has a distinctive twisting to it and they are short as in your image. From what I can tell, in your image the movement is not quite the same and also the bacteria seems to sometime look like a clothespin.  I hope Dr. Elaine can weigh in on this one. 

Are you using the oil immersion lens for your 1000x magnification?  The flagellate image is awesome.  As for the would be ciliate, again, I have not seen this kind of shape and in your image I was not able to identify any cilia (hairs).  But I cannot say definitely what it is, though I wonder if it isn't a small nematode?

I hope to be sharing pictures and asking questions soon!