Monday, November 30, 2015

Washington State University Ag Extension Compost Tea Webinar Revisited

Soil without Biology is simply Geology
Well the Webinar put on by Washington State University Ag Extension gals (Lynn Carpenter-Boggs Associated Professor of Sustainable and Organic Agriculture at WSU & Catherine Crosby who is a PhD candidate for Soil Science also @ WSU) provided very informative material for recipes regarding compost teas and how to use them finally them came and went without all the advertise upset by individuals with a vested interest in industrial science. With all the advertised potential for anti-science rants coming from the WSU Garden Professors over the potential negative harm this Webinar was going to cause in the public's mind in creating a less than scientifically minded landscapers/gardeners, what actually came across in this Webinar was totally opposite of what most followers of the Professors would have expected. The Compost Tea Webinar was very intelligently presented, honestly & refreshingly informative in educating listeners that this was a new field of research yet to be thoroughly tested scientifically and the need for caution where some potential areas of both dangers and benefits where carefully and respectfully pointed out minus the usual smug sarcasm often experienced with this subject. For the folks who have yet to watch the Compost Tea Webinar, here it the link and keep in mind it's about 75 minutes in length.
WSU eXtension: Making and Using Compost Teas

First off I'd like to confess, I've never really been one to actually use compost tea. My Mum has made her own and swears by it. And the plants in the yard never looked better. The closest I've come to using a type of compost tea is using Kelp or Seaweed Extract and Liquefied Fish Emulsion diluted with water for a tea used for watering newly emerged seedling and again after transplanting them into one gallon containers. But this was limited as they were always soon outplanted. However according to Catherine Crosby, my version of the compost tea still wouldn't qualify as real compost tea because I never left the mixture ferment beyond one hour. True, after mixing I always used the blend immediately. Mostly my purpose was to provide slight nutrient availability to small seedlings while containerized as I though using any type of pellets, crystals  or other was simply too rich a diet for small seedlings and would be nothing more than waste. I must say this practice was always without fail successful for the need intended. But all in all I thought both women who were the presenters of the Webinar did a wonderful job, NEITHER saying anything controversial nor unscientific as the WSU Garden Professor criticism always hyped. Both were very upfront that there really is not a lot of scientific data on compost recipe blends, successes, etc. They both did quite a bit on cautioning people on potential for unhealthful conditions if done wrong [like creating an anaerobic tea. They strongly insisted that no human or other animal waste contaminants be used and that aeration of the mixture was imperative to create an aerobic compost tea as opposed to an anaerobic tea which would smell and probably have the wrong type of microbes present. One of the other interesting things mentioned was that compost tea is being look at as a possible experimental pesticide. Now this was interesting, but let's define pesticide here for a moment. Pesticide could be the elimination of anything that would do harm to a garden, urban landscape or commercial farm for which numerous synthetic chemicals would otherwise be employed like insecticides, fungicides, herbicides etc. Specifically here both woman, but especially Lynne Carpenter-Boggs alluded to the fact of compost tea having a potential for preventative suppression of pathogens, blights and powdery mildews on foliage, but that more experimentation and testing be done for the correct formula.

Again on this association of Compost Tea as being a possible pesticide, I have found several stories around the net about whether or not compost teas will kill bugs. Let's be honest, when the mere mention of the word "pesticide" is always used, the #1 thing that comes to folk's minds are Bugs. Almost no one will consider the full definition range of what the word actually means. I mean there are also blight, mildews, viral infections and other bacteria diseases that should also come to mind, along with unwanted weeds. The term pesticide encompasses all those things. But will compost teas kill bug ??? Absolutely not, unless one fell into a five gallon pail of your compost tea and drowned because it couldn't climb out. Mostly here compost tea is used as a soil and foliage inoculent and that's it. It was interesting to me the other day when someone contacted me and reported that the members/followers over on the Garden Professors Blog's Facebook community pages were discussing once again the controversial Compost Tea Webinar from WSU. Okay, but there was nothing controversial about it. The problem is many of these Garden Professor followers & Garden Rant types they attract like to hunt down and post stuff which may be of a controversial nature just what kind of outraged they can get from one of one of the Garden Professors or fellow sel-proclaimed Master Gardeners. One individual who seems like a nice enough guy, who also patterns his own blog as a fable and myth buster for gardening posted this statement to see how Linda Chalker-Scott would react. 
"I found the following statement very interesting. Why is this true,  "compost tea is considered to be an experimental pesticide" - Robert Pavlis
Well she didn't disappoint. Took everything out of context and in fact didn't think thoroughly about what was actually said [going purely off the vague quote mine mentioned in the Webinar and I suspect that was because she hadn't actually viewed it, before she blurted out:
"Legally there is no such designation. It's not registered anywhere as a pesticide so using that term is not appropriate." - Garden Professor, Linda Chalker-Scott
This was unbelievable. This actually exposes the fact that she didn't actually watch the Webinar before making this comment. Even the quote mined reference should have been a clue they never stated such a thing when all they said was it was being considered as something experimental. Mostly her uninformed response played off her preconceived prejudice and biases against compost teas. No where did EITHER women, Catherine Crosby or Lynne Carpenter-Boggs EVER say compost tea was a registered pesticide let alone a simple natural pesticide. They both emphatically stated  it was being considered as an EXPERIMENTAL Pesticide, which means that someone is probably merely experimenting with various formulations, possibly involving some sort of specific microbes and/or natural extracts to trigger an immune response in plants against pathogens. That's all there was folks, they never even hinted that compost tea should ever be considered a registered pesticide. But it get's even worse, when a member named John A Perazzo asks for clarification on the term pesticide whom I assume think like many others [including Ms Chalker-Scott] that these ladies were talking insect pests.
"Is there another word in English that distinguishes something from chemically killing pests (a pesticide) to say, starving the pests to death?" - John A. Perazzo
So rather than doing her own homework so she could clearly ascertain what both Catherine Crosby and Lynne Carpenter-Boggs actually meant by using the term pesticide, she assumes like everyone else, they are saying compost tea will kill insects.
"Not really, It doesn't matter how the pest dies - it makes the agent a pesticide. (And just to be clear - compost tea has no consistent, demonstrated pesticidal effect.)"        Garden Professor, Linda Chalker-Scott 
Now when Catherine Crosby first made mention of "considered as an experimental pesticide", I instantly knew exactly what she was probably alluding to. In fact later on in the Webinar when Lynne Carpenter-Boggs took over and said basically the same identical thing, but also she further clarified what was meant and it totally confirmed what I already knew. Here is what Lynne Carpenter-Boggs actually said and clarified at the 17:30 mark of that Webinar:
"In the last portion of this talk we'll talk about compost tea as a disease suppressant and some of the research that's been done in this area. And then get into the legality of using compost teas. The first thing I want to say about what Cece mentioned about using compost tea as a disease suppressant or disease control is that this is being considered as an experimental pesticide and that we are NOT recommending the use of compost tea for use as disease control."
 "The one thing we can say about the research out there is that the results are mixed. There are some studies showing that a particular compost teas have suppressed particular diseases and there are a few studies that suggest that compost teas have actually worsened disease. Sometimes we also see enhanced plant growth and the reasons a particular compost tea enhanced plant growth is that they may have contained some nutrients. There are also some studies showing that some compost teas contain plant hormones, so that's another method by which they may be increasing plant growth in some studies. There are some studies which show reduced harvestable yields as well as some studies which show increased harvestable yields. And some studies which show no noticeable effects."
"As Cece mentioned, there are many many kinds of compost teas, there is no single compost tea. So it's not surprising that when studies pop up that will show in compost teas, the results are going to be really different. Then of course every disease is going to have a different life cycle and the teas have been used in somewhat different ways so that it should be a surprise that results are really mixed. There needs to be a lot more work done before any kind of recommendations can be made. So with those caveats there are dozens of studies which showing  that the use of compost tea reduced or controlled certain diseases."  - Lynne Carpenter-Boggs
I'll leave it there as there is so many more incredible things she next talks about as far as from a mechanisms standpoint which I gravitate towards anyway. She actually shows us in the video the exact same slide photo of a fungal species called Trichoderma attacking a pathogen by actually boring holes into it. Just like the one here on the right. Trichoderma is not necessarily as glamorous as other fungi with those wonderfully tasty and beautiful truffles, but rather looks more like the fungal mold in your bathroom build up. I just finished writing about this fungi the other day. (Here)  The reason I am writing about it is because it produces some incredible amazing epigenetic effects depending on the soil environment or ecosystem it is residing in, the different plants etc and all the while triggering on switches to plant genomes to produce chemical immune defense products to ward off pathogens before they arrive. In fact Lynne also names a naturally occurring commercially produced product called Harpin Technology which is a protein in the form of an RNA protein chemical which can be sprayed on the outer surfaces of plant foliage to simulate an attack which triggers the plant's immune system chemical defenses. Here is something further that Lynne Carpenter-Boggs referenced regarding potential for the right formulation of compost tea being utilized as a systemic drench which would act as an systemic acquired resistance inducer for triggering the plant's own immune system response prior to being actually attacked.
"There can also be stimulation of plant responses and we'll go into more detail on this one because it's really interesting. And there also be an interference with the disease life cycle. In some cases for instance we see that diseases need to build up to a high population before they turn to a pathogenic stage of their life cycle and the use of compost teas again partially by means of microbial competition can simply reduce the likelihood that pathogenic population reaches a high level in that life cycle of pathogenic phase. So we'll talk a little bit more on that systemic acquired resistance and compost teas are definitely not the only kind of  material that's being researched and being used to stimulate a systemic acquired resistance in a plant. What this is like is a sort of "plant vaccination" and you're stimulating a plant response prior to a pathogen attack. Now plants can make and use a number of defense compounds to protect the cell wall or to  break down the pathogen. We can look at what happens in the plant apply an inducer material which in some cases might be a compost tea, but also there are commercial products like Harpins that can induce this response."

This was awesome that she referenced commercially available Harpin products. I first stumbled upon the Harpin Protein Technology when I purchased my mycorrhizal inoculation products from Plant Health Care Inc (PHC) out of Pennsylvania, if I remember correctly. This Harpin is one of a class of proteins occurring in nature by certain bacterial plant pathogens. Like the epigenetic trigger inducing immune system response effects on a host plant whose root system is colonized with Trichoderma virens which I wrote about the other day (Here: Trichoderma virens systemic inducer) , this Harpin protein can also elicit a complex natural defense mechanism within plants. While most of the conventional pesticides we've all used in the past act directly on the target pest, this Harpin protein when it comes in contact with a plant's foliage, according to the developer of the product, elicits a protective response in the plant to producer it's own defense compounds that makes it resistant to a wide range of fungal, bacterial, and viral diseases. Because the use of Harpin protein has the potential to substantially reduce use of more toxic pesticides, especially fungicides and certain soil fumigants, such as methyl bromide. And I hate methyl bromide as I've written about in the past regarding sterilizing seedling growing media to prevent damping off in regards to emergence of the seedlings who rot at the root collar just at the soil level. (Read Here)

Plant Health Care Inc., (PHC)
In nature, this Harpin protein is produced by an organism called,  Erwinia amylovora, which is the same bacterium that causes the disease fire blight in apples, pears and also several of the native California plants I have used and planted like California Coffeeberry. The commercial production of this Harpin Protein actually comes from a weakened strain of Escherichia coli has been genetically modified to produce Harpin on a commercial scale. Commercially produced Harpin protein is identical to the protein that occurs in nature. E. coli K-12 which is considered to be a non-pathogenic, nutritionally deficient bacterium which is supposedly unable to grow in the environment. Of course we've heard this before, but who knows. This Harpin product is concentrated from the growth medium of the genetically modified E. coli, and the bacterial cells are killed and removed from the marketed product. Again, all it takes is that one rouge bacterium that gets free, so who knows. Plant Health Care Inc was not the original inventor and Patent holder, I believe they purchased this technology from another company (Eden Bioscience Corp) and then started their own commercial production. The product I believe was released back in 2002 as Messenger® by Eden Biosciences. About this 2006 when I moved to Sweden, the folks at  (PHC) were becoming distant and disconnected from their original end user clientele. With the retirement of their chief science officer Dr Donald Marx and later the death of his wife Faye down in Frogmore South Carolina where they use to hold regular workshops teaching landscapers, farmers and others on the microbial world and how it operates and functions and how (PHC) had the products to replicate management of commercial plant operations as a viable ecosystem, but this educational program came to a halt. Finally for me what broke the proverbial camel's back was their agreements with Monsanto in licensing for this generic engineered Harpin technology. There was more focus in doing business with other corporate giants and also becoming a corporate giant themselves where the push and marketing for stock shares was what most of their website was all about. I tried contacting their UK Office for info on obtaining product here in Europe, but the guy I dealt with wasn't overly interested nor helpful in that regard. He promised to send me a product list and pricing but I never received them. The end user landscape division of Retail product sales was sold off to Lebanon Turf , also from Pennsylvania which to this day still sells PHC products. I believe the products are most likely still excellent products, but I simply switched over to Mycorrhizal Applications Inc out of Grant Pass Oregon.

WSU - Lynne Carpenter-Boggs
Here is my point in giving you a bit of history about all of this issue with the mention of "compost tea considered an experimental pesticide" and the Harpin Technology. Clearly in that WSU eXtension Compost Tea Webinar, both Grad Student, Catherine Crosby and soils microbiologist, Lynne Carpenter-Boggs did indeed mention this briefly a few times, but made sure everyone knew this was considered experimental. There was no dogmatic insistence that it was considered a registered pesticide. That exposes the fact that Linda Chalker-Scott hadn't really watched the Webinar at that time, otherwise there would be no reason to make the accusation. Also the present Lynne Carpenter-Boggs was the one who brought up the Harpin technology by name and the obvious reasons were that proteins manufactured by some bacteria can have a triggering effect in turning on the plant's immune response to contact. If indeed some researcher did one day discover a safe bacteria which could be added to the tea that would elicit such a mild response of plant immune system boosting then so be it. This is why ongoing studies and research for just the correct formulations would indeed be considered experimental, because that is exactly what is going on. 

Interestingly, had Linda Chalker-Scott actually watched this Webinar and heard Lynne's reference to Harpin Technology, she would have instantly known what Lynne was referring to because guess what ? Linda Calker-Scott has in the past several years ago written about this very Harpin Protein, Eden Bioscience and their brand name product Messenger® and did so in the most negative of reviews. Many of the studies she cites date back to the early days, like the one from Cornell University. The problem however is  when I go back to Google those research studies, the dates of the studies are anywhere from 1999-2000 to 2003. It's an entirely new ballgame since 2010 and newer upgraded products by several companies exist today. I'll post her link to this Myth article she has and incredibly although the link shows an update of March 2015, her material used is mostly negative against Eden Bioscience and Messenger® from earlier studies which have nothing to do with today's products. Apparently these products have been successful through improvement. But she hasn't updated at all, so the only myth is an earlier personal biased take on this product and it's claims. Again, the Harpin Technology was purchased by PHC in 2011 and newer upgraded products are AXIOM and other brand names and even the great Monsanto has purchased licensing from PHC to manufacture their own version of Harpin products. This makes sense from a money making standpoint, because when all your other technologies with GMO plants and agro-chemicals have greatly disrupted natural underground microbiological processes, then an artificial means of systemic inducement of plant immune systems makes more financial sense. the bottom line is that there are no science-based or peer-reviewed updates regarding Myths/Facts of Harpin on her site.

Again, neither of those presenter ladies in the Webinar never made such a dogmatic statement that compost tea is an official pesticide. Once again for clarity, this is why firmly stating that compost tea was being only considered an experimental pesticide and NOT a registered pesticide as Linda Chalker-Scott in ignorance posted in response on her own forum. It is clear to me that these Garden Professors didn't exactly listen and /or pay close attention to the entire Webinar if at all at the time it was released. Their ranting followers have much of the same selective reading quote mining and comprehension problem as well. Many of them even have their own websites dedicated with nothing more than garden ranting about landscaping myths and/or fables and championing themselves as professional debunkers.

Cece Crosby
One of the disappointing comments was where someone questioned how really scientifically qualified the presenters really were. The qualifications of Catherine (Cece) Crosby were brought up because she is only a Grad Student. Seriously, so what ??? They both did a very professional job in educating the public on things they may have never considered and the real unprofessional conduct came from those who have previous bias and prejudice against compost tea, selective quote mining and a sort of mystic ability to read between the lines. Funny, you know, anytime I ever tried reading into a text between the lines, all I ever found was empty space. Look, I'm also not overly interested in compost tea as a foliar spray or possible pest control. That doesn't mean it couldn't work given the correct formulation and handling of how it was made. I believe, like some of the things these Garden Professors stated, about letting compost do it's job under trees and shrubs when every time it rains a new weak batch of teas are produced for the benefit of the plant. Now that make work wonderful in wetter Washington or Canada, but what about the southwest where far less rain falls ??? However, I have no problem if someone wishes to do these things. In fact I am very impressed with Harvard Yard's professional and successful use of compost teas on their lawns. The lawns and soils vastly improved and for me as a former landscape head gardener with a commercial property management company who actually hated lawns, I love the fact that Harvard Yard's non-chemical (synthetics for those who love definition shell games) methods kept the grass greener and made it grow slower. That translates as less mowing and dealing with waste and far less money being put out for massive amounts of chemical inputs. 

photo: Getty Images
The Garden Ranters set out to paint a unfair picture of people who chose to take a holistic approach as mad citizen-scientists working behind the scenes in one of their own bathtub operations or new-agey Luddites promoting Voodoo science for profit. I find many of their rants as nothing more than time wasting nonsense created to entertain an elite few within a certain specific cultural setting who have little else to occupy their time for the benefit of others. So the question now is, "How can the average person really know for a certainty just what is the right way to design, create, install and maintain your garden, landscape or even commercial Farming operation successfully and free oneself from the shackles of corporate agro-chemical recommendations ? First of all, it is absolutely NOT necessary for you to study and compare every so-called myth or fable advertised and promoted out there [this even includes many of the heavily advertised science-based & peer-reviewed hype by Industrial Science business interests] or even weeding through the plethora of self-help book teachings of all the many Garden/Landscape Gurus out there. You need only learn about whole complete natural plant community ecosystems and how really function and maintain themselves. Very few people do this anymore and this includes numerous scientists stuck in a Lab away from the real life outdoors. This also requires the average person getting themselves outdoors which is imperative. It's not enough to read the popular books [even scientific textbooks] which exclaim how they have the peer-review, science-based and settled consensus science to back them up. You may find that such recommended techniques will probably need specific tailoring to your own specific region. Look for healthy viable horticultural practices that biomimic or replicate how nature actually functions and operates out in the field. So again, you don't have to read and study every popular garden fad that makes the internet rounds. So then now what ???

To illustrate: In many lands, there is a problem with counterfeit money. If you wanted to pursue a career as a professional whose job it is to expose what really was false counterfeit money, what do you think would be the correct way you should go about it ? Would it really be necessary memorize every single kind of counterfeit money [garden myth, fable] that has ever been produced ? No. Your time would be better spent if you studied what real money actually looks like in great detail. Perhaps after you knew what real money looked like, you could then be in an educated position to recognize and identify what a true counterfeit looks like. Similarly, when you learn how to identify how whole natural plant ecosystems really work and function, then you will easily  recognize which  advertised horticultural practices [science-based or otherwise] that are the true myths and fables without all the wasted time of proving the claims wrong. It's also not necessary to be insulting or employ derogatory name calling by insulting others with labels like "pseudo-science", "anti-science", "practicing Voodoo Science" or calling others Luddites just because they do something different than you. Just leave others alone and offer the sounds advice you know for a fact that works.

In our world it seems that negativity sells. News Reports daily are loaded with negativity because for whatever reasons the average person today seems to gravitate towards that type of reading content. If a media outlet posted only positive news, they wouldn't get that large target readership needed and low ratings translates as no advertisers which means no money. I can even admit myself that when I do an article on some injustice or irresponsible practice of some corporate methods hurting the environment, I get more reads than if I write about beneficial plant findings or landscape tips. As a prime recent example, I wrote about an amazing plant which most people in Southern California demonize as of little worth. It is viewed as dull, mundane, a rangy chaparral plant of no real value other than control burning and yet it is one of the most abundant chaparral plants. The plant is Ademostoma fasciculatum otherwise known by common names of Chamise or Greasewood. This plant has incredible physical characteristics at preventing of erosion, it will grow in many places other plants will not or cannot grow and is an excellent forest "nurse plant" which facilitates plant community succession. I wrote that over two month ago and have 131 reads. And yet, I just a few weeks ago wrote about the negative attitudes of these garden professors against the people who run and maintain Harvard Yard's landscaping about a few weeks back and have over 500+ reads. Here is the point, whatever is insisted upon as fact for no other reason than it is labeled as "science-based" and/or "peer-reviewed" can itself actually be in reality factoidal. So when it comes to garden, landscaping and/or farming practices and advice, then test it out for yourselves people and do this by making comparisons on how nature really works as opposed to industrial scientific shortcuts design for cash lining the pockets of an elite few with an attitude.
I'll post some reference links as promised and you can make up your own minds. Also, here is my previous post about the Garden Professor's unfair and derogatory insulting name calling rant  against the professional landscapers in charge of Harvard Yard's Soil Project who have 80+ acres to maintain at Harvard University:
The Arrogance and the Ecstasy: The difference between Good Science & Bad Science when it comes to Soil Health
"This assumption [that scientific institutions have a peculiar epistemic reliability] is at best naïve and at worst dangerous. If any human institution is held to be exempt from the petty, self-serving, and corrupting motivations that plague us all, the result will almost inevitably be the creation of a priestly caste demanding adulation and required to answer to no one but itself. 
— Austin L. Hughes, The New Atlantis, Fall 2012
Now to be completely honest & fair, as I've stated, I do believe in many of the things said by Linda Chalker-Scott and the practices she suggests. But the Blog and Garden Professors Forum have just gotten out of control with pouncing on every little burp or hiccup that is perceived as an imaginary  flaw or mistake.
 Here is something she wrote that I do like [well 90%] about Mycorrhizae. It fits in with most things I have observed and even read about. The main disagreement I have is she is one of these "You never need to inoculate the soils because the fungi are just out there in the soils". WRONG, conventionally maintained agricultural soils which have for decades followed the industrial dogma are virtually devoid of the healthy organisms that benefit soil building qualities. Same with urban landscapes where again, people have maintained their landscapes/gardens using the same failed synthetics as commercial farms. And this is especially true where new housing development has property pads created from sterile sub-soils, often made of nothing but decomposed granite with zero organic matter. So here is a link she provides which I mostly do like.
MYCORRHIZAE: So, what the heck are they, anyway? 
Garden Professor Myth and Fable Links:
The Myth of the Magic Bullet (Harpin - old & outdated but still pimped)
Plant Health Care Inc and Lebanon Turf
Some viable alternatives to using genetically engineered Harpin Proteins - In the USA the Knotweed extract product is marketed under the name Regalia®
Marrone Bioinnovations: "Regalia" (USA brands)
Marrone Bioinnovations: "Regalia RX" (USA brands)
Over here in Europe, the Knotweed extract product is marketed under the name Milsana®

Wednesday, November 25, 2015

How Many Beneficial Functions & Services can be found in just one Fungi Species ?

So let's focus mainly on one fungi species in particular and two varieties,  Trichoderma virens and Trichoderma harzianum
Image: US Department of Agriculture
Trichoderma harzianum

Image: Manidharma Biotech

Trichoderma harzianum
The photograph above under magnification is beautiful, almost like a snowflake developing it's hexagonal branching. These see though glass looking structures are called conidiophores which are the specialized branching hypha of the fungi which also produce spores. The photo at right here of the fungi specimen in the glass petri dish looks more like that common yucky mold folks find in the kitchen or bathroom where one wants to reach immediately for that chemical spray to kill it straight away. Yes, Trichoderma is not as sexy looking and/or  delicious as some of it's culinary cousins, but it's an incredible workhouse of the microbial community. We could compare them to the lowly payed blue collar laborer who is the hard working backbone of any society. Yes there are more well known rich  attractive celebrity types [sports stars, Hollywood movie stars, Rock Singers, etc, etc, etc], who are better known for no other reason than they stand out among the average person, but these people would be absolutely nothing were it not for those blue collar folks [plumbers, carpenters, sanitation workers, maids, gardeners, farm hand  workers, etc etc etc] who keep society's infrastructure in top working order. And so that is exactly how this lowly inconspicuous, but incredibly numerous hard working fungi are to the natural world's various larger than life beautiful plant community ecosystems. These Trichoderma varieties and/or strains of fungi have incredible abilities for the benefits of both plant immune systems and the soil health and nutrition in general by helping to regulate improved growth even under stresses. What got me curious originally about the Trichoderma was what I read on my last package of MycoApply Soluble Maxx which had on the ingredients list 19 species of mycorrhizae (9 endo & 10 etco), 12 species of beneficial bacteria and 2 species of Trichoderma. Trichoderma ??? I had never explored these before, so I thought it would be fun to find out what they would add to my landscape's ecosystem. At first I looked at Trichoderma harzianum to see what benefits have been realized in the landscape, agriculture, garden, etc. Then I also looked at Trichoderma virens which also has some incredible effects it can trigger on plant growth and their immune systems. Use of visual aids are always good in educating people on certain things they consider mostly BORING! So apparently both these fungi can have a huge impact on helping the plant fight off pathogens. 

Plant root colonization by different Trichoderma strains can activate in the plant a systemic defense response that is effective against a very wide range of plant pathogens. A plant's immune system also has a wide variety hormones which play pivotal roles in the regulation of the defense signaling network that leads to the processes of systemic resistance triggered by beneficial micro-organisms. One of the most important of these chemical defenses, jasmonic acid and ethylene (like ethylene gas for fruit ripening) signaling pathways are generally essential for triggering these immune system responses. However, this Trichoderma Immune System Response (TISR) is believed to involve a wider variety of signaling routes, interconnected in a complex network of cross-communicating hormone pathways. For example the experiment above with tomatoes grown in Greenhouses is a perfect example of where Trichoderma harzianum can trigger an immune response  against a leaf pathogen called Botrytis cinerea. Root colonization by the Trichoderma harzianum provided these tomato leaves with much more resistant to Botryis cinerea independently of major effects on plant nutrition. You can see the results from the above images which show tomatoes grown under greenhouse conditions which displayed vigorous health compared to the one which succumbed to the infection. Now I've never personally experience such infection on any tomato leaves in gardens I've raised, but this type of fungus disease is much more common in a more humid greenhouse environment than outdoors. However this disease is more common among grapes and strawberries. However, once again it's the closed in humid greenhouse environment which makes this a challenge and this is important because these days so much of our vegetables in and around urban areas where land is scare are produced. So how kool is this that the Trichoderma fungi can create the necessary hormonal signalling network behind the systemic resistance induced by Trichoderma harzianum in tomato instead of farmers having to rely on the traditional cocktails of chemical fungicides ?
Model: Department of Microbiology and Symbiotic Systems, Granada Spain
This animated model shows very simply the two sides of a tomato plant. One side colonized with the Trichoderma and the other side not. The colonized side triggers the messaging system and epigenetic switches turned on for the manufacture of important chemical compounds to ward of pathogens and even herbivore attacks by insects. Although mainly this was a study on Greenhouse Tomato plants susceptible to the fungal disease. Let me take one other variety of this fungi, Trichoderma virens as pictured below. 

Photo courtesy of: Charles M. Kenerley and Prasun Mukherjee.
"Coiling of Trichoderma hyphae around Rhizoctonia (a basidiomycete pathogen). The coiling response of T. virens is induced by the presence of host hyphae and precedes penetration of the host."

Photo Courtesy of Dr Randy Martin, Bioworks, Inc.

"Scanning electron micrograph of the surface of a hyphae of the plant pathogen Rhizoctonia solani after mycoparasitic Trichoderma hyphae invades the pathogen by boring holes into the pathogen with various cell wall degrading enzymes"
"Trichoderma species are free-living fungi that are common in soil and root ecosystems. They have been widely studied for their capacity to produce antibiotics, parasitize other fungi, and compete with deleterious plant microorganisms. Until recently, these traits were considered to be the basis for how Trichoderma exert beneficial effects on plant growth and development. However, it is becoming increasingly clear that certain strains also have substantial direct influence on plant development and crop productivity. Trichoderma enhancement of plant growth has been known for many years and can occur in axenic systems or in soils"
Image: Cornell
"In maize (Corn) plants, Trichoderma inoculation affected root system architecture, which was related to increased yield of plants. Reported effects include enhanced root biomass production and increased root hair development. The root system is important for plant fitness because it provides anchorage, contributes to water use efficiency, and facilitates the acquisition of mineral nutrients from the soil. Many lines of evidence strongly support a role for auxin in the regulation of root system architecture. Application of natural and synthetic auxins increases lateral root and root hair development, whereas auxin transport inhibitors reduce root branching." 
"Conversely, increased formation of lateral roots has been observed in Arabidopsis thaliana (or Thale Cress) mutants with elevated auxin content . . " 
" . . .Despite auxin being a major player in root growth regulation, little is known about its role in plant growth promotion by fungi."
"To elucidate the signaling mechanisms by which Trichoderma species promote plant growth and development, we evaluated the Arabidopsis response to inoculation with two Trichoderma species, Trichoderma atroviride (formerly known as Trichoderma harzianum) and Trichoderma virens. The two fungal species were found to promote Arabidopsis seedling growth under axenic conditions. Plant growth promotion elicited by these fungi correlated with prolific formation of lateral roots. A role for auxin signaling in mediating the observed developmental alterations by Trichoderma virens inoculation in plants was inferred from tests using the auxin-responsive marker constructs. We further show that Trichoderma virens is able to produce the indolic compounds indole-3-acetic acid (IAA), indole-3-acetaldehyde (IAAld), and indole-3-ethanol (IEt), which may play roles in mediating plant growth promotion by this fungus."
Important terms to define and explain from the above research article:
"Auxins" a plant hormone that causes the elongation of cells in shoots and is involved in regulating plant growth. Basically can encourage growth by means of a signaling process as seen in the examples of thick Corn root infrastructure.
"Jasmonic Acid" (JA) and its derivatives are lipid-based hormone signals that regulate a wide range of processes in plants, ranging from growth and photosynthesis to reproductive development. In particular, JAs are critical for plant defense against herbivory and plant responses to poor environmental conditions and other kinds of abiotic and biotic challenges. Some JAs can also be released as volatile organic compounds (VOCs) to permit communication between plants in anticipation of mutual dangers.
"Axenic" In biology, axenic describes the state of a culture in which only a single species, variety, or strain of organism is present and entirely free of all other contaminating organisms. The earliest axenic cultures were of bacteria or unicellular eukaryotes, but axenic cultures of many multicellular organisms are also possible. Axenic culture is also an important tool for the study of symbiotic and parasitic organisms in a controlled manner.
Now that last defined term is interesting in that in studying the subject here of Trichoderma, we want no outside contamination of any other organism within our experiment. We want to observe the effect the Trichoderma fungi alone has on plants. Clearly the effects of Trichoderma appear to provide multiple positive benefits. But now comes the tricky part. It's one thing to have it work in a lab, but how well will these same functions and benefits work in the field. Well, you can read on further down below. However, when any of these Mycorrhizal Inoculent producing companies are experimenting for that magical powder or solution as an inoculum, sometimes the desired results may not translate as well in the field tests as they did on paper in the Lab. Why ?? Because once in the field, that single organism that did all those wonderful things now has to compete with a plethora of other like organisms. While there  may have some colonization of a certain specific target species of your favourite fungi on some roots, the effects could be minimal because of the competition already occupying root space as compared to if the fungi were alone. So there are going to be many more challenges in research and experimentation on finding a beneficial as well as tough enough fungi to fit into your magic inoculum product. Can you imagine where we'd be if science decades ago had spent more time observing, admiring and replicating nature as opposed to viewing it as flawed, imperfect and so badly designed that the route taken was to genetically manipulate imaginary improvements to plants while totally ignoring Nature's optimization performance enhancing after market add ons ? 

 The other two terms up there Auxins and Jasmonic Acids in which the Trichoderma can act as an inducer for the production of these growth enhancing and pathogen suppressing immune system tools are also wonders to behold, especially in the light of the successful experiments mentioned below. Drought Stress tolerance enhancers, growth and nutritional enhancers, aside from the pathogen suppressing elements against diseases and insect herbivore attacks. Why Science is still trying to decipher how the hormonal signalling network behind the systemic resistance induced by Trichoderma harzianum in tomato actually works. Yes, where would our world now be if the direction of Science went here instead of artificial money making industrial opportunities ? One thing is for sure, most of the industrial giants would be so giant, especially if Farmers ever gained the knowledge that they could accomplish successes by changing practices and making money by not having to fork over hard earned money to others for basic substandard environmental destroying products.
 Here is an interesting example below of a company that has tested Trichoderma on  Corn in the field for drought stress. 

The company ABM with Dr Gary Harman PhD is a new one for me. I have never used their product and I am not necessarily endorsing it. You will have to do further homework. What interests me here in the video below are the results of drought stressed Corn left to it's own without the aid of further water supplementation where two scenarios of one control or untreated field and one field treated with this company's Trichoderma product. It's four minutes long and you'll have to watch it to the end to get the entire story. I've also posted a very wonderful easy to follow article written by Gary Harman which should illuminate further the benefits of this one particular Fungi.

Frankly I find this stuff fascinating every time I stumble across other folks with kool experiences. But there are some precautionary things you need to keep in mind. People want an instant acting magic powder or liquid Elixir to perform insta-poof results on their plants which often times is all they get from the agro-chemical companies. This isn't about instantaneous results. I've given this illustration before. A person who becomes a sports star, Hollywood Celebrity or political darling doesn't do so over night. They work hard at their career often sacrificing a real normal life, even family to obtain that immortality of celebrity status. Many take decades accomplishing this. Then in a moment of weakness, they do something controversial, stupid and outrageous behaviour-wise and their career slips into the toilet. It may take a very long time to heal wounds and erase the damage done almost overnight. Just maybe they can rescue their career out of the toilet. The natural world is the same. It has taken the natural world 10s of 1000s of years to develop an Earth into a beautiful paradisaic state. And yet in little over 100+ years (1914) of so-called scientific enlightenment to the present, our Earth and it's various life sustaining mechanisms are now on the brink of total collapse. My field of interest has always traditionally been ecto-mycorrhizal fungi and experimenting with various species of these fungi with specific species of plants and under varied environmental conditions. Delving into the Endo-mycorrhizal world and all other associated beneficial organisms has really been a further eye opening reward. The results not just through reading, but practical application which have brought me personal successes has been rewarding. 

The Biostimulants companies have got to better educate the public in common everyday language minus all the intellect speak if wishing to reach the average person. With Farmers, don't tell them in a sales pitch  that if they use such n such miracle product they will find sure success. Explain the truth of the matter in simple terms. Tell them that damaged soils do not heal overnight in one season. Seriously, many people actually believe this. It may take two or three years, maybe more. Restoring a biological degraded field which percolates a half inch an hour of rain needs time. Healthy biologically rich soils should be able to percolate up to 8 inches an hour. You can accelerate that time not only through a healthy inoculation program, but planting as much as 20 different species of perennial prairie pasture plants which will further enhance the microbial community underground. The more species of plants & Mycorrhiza species will quicken the healing. Same with the Ecot-Mycorrhizal World. Take a look at the pine seedlings with the small Pisolithus tinctorius truffle in the photo above right. Time and again in my experience [and I have written about this on numerous posts], this ecto-mycorrhizal fungi will form a truffle two weeks after I inoculate an established or newly planted pine or oak tree in the summertime. And every time a single truffle will appear at the size of an average adult male's thumb in about two weeks, which lets me know the fungi has colonized and is feeding off the carbon of it's host in order to make this thumb sized truffle. Now, what a person should never expect that first year is to see a dramatic difference in the growth and vigor of the host plant's foliage. Mostly it will be in a neutral state. However by next Spring after Winter rains, you should expect an explosion of growth with larger that previously experienced foliage size. This has been my experience every single time. Now how often do you get a Biostimulant Company Salesman telling you such pertinent information ? Same with Farming and Endo-mycorrhizal colonization of crops. How many Biostimulant company salesmen are going to take the time to explain to prospective clients who just happen to be farmers how they should first build a healthy microbial community in the soils before they plant a money making crop ? Almost none. I know because I have gotten feedback from Farmers who were sold a story which failed to deliver as promised  that first season because some salesman actually had no hands on experience in practical application of his or her own product. It took decades to destroy the microbial community and it will take time to re-establish, but knowing a few simple tricks can speed that rebuilding process up. Now take a look at this moving image below.

Illustrative animation by
I've always loved this GIF (Graphics Interchange Format) from the very first time I ever saw it. Though it was created for an entirely different purpose by it's creators, I found probably an even more important illustrative usage for it. The environment's various epigentic effects on how an organisms various DNA components and informational content are expressed in various different ways for adaptability and survival. Take the strings of letters, making words and eventually sentences of meaning in the GIF. Now look at those shadowy hands influencing how those letters which make up words will be laid out and expressed differently depending on the environmental context of life's chapters in a book. Maybe the book can be viewed as life in general on earth. The chapters of that book being various ecosystems [deserts, tropical forests, Temperate forests, Boreal forests, Mediterranean Chaparral systems, etc]  as defined by climate with localized weather event like droughts (heat, cold, humidity, etc], freezing rains or snows [possible seasons], flooding events, perhaps geography or elevation, etc. Further the changes could be influenced by predators, invasive species totally foreign to the exiting environment which demands change or go extinct. In any event, such environmental conditions trigger responses through an organism's receptors or sensory mechanisms which in turn trigger epigenetic switches to be turned either on or off depending on the requirements. These shadowy hands and fingers represent the context of the environment working and influencing how genetic information within DNA is expressed. I've always loved Alfred Russel Wallace's explanation over Darwin for how the environment can influences specific mechanized change as compared to the silly use of the term, "Natural Selection" which is so often depicted as some sort of mystic Tinker Bell which accomplishes amazing changes in mysterious inexplicable ways. The term "Natural Selection" is often used as a lazy default answer in discussion where no real details are available or can be identified for further intelligent explanation of change. Request further information and details on the subject in question and you generally are bombarded with a plethora of derogatory insults, foul language and insulting name calling, all of which apparently are the new enlightened way of discussing and disseminating information about scientific matters these days.

But on the intelligent side of epigentics and it's work on triggering specific switches within even the fungal organism Trichoderma itself, this is where the subject becomes much easier to understand from an organized mechanisms standpoint and practical application by means of biomimicry. Google this organism through various scenarios of environments and plants it colonizes and all manner of epigenetic schematic effects come up. Depending on soil environment and the specific plant it chooses as it's host, there are a number of different things it can accomplish and influence through the biological messaging network. This is the way the plant health care industry should have pursued things years ago and they chose not to for strictly financial gain reasons. It's important for landscapers, gardeners and farmers to understand even to a limited degree of  how their practices [Good, Neutral or Bad] can and do have an important epigenetic gene expression effect on their living landscape. For example, in the modern conventional excessive use of synthetic chemical fertilizers, there is an epigentic effect on a host plant shutting down it's signalling chemical compounds which triggers the ongoing colonization message to mycorrhizal fungi which in effect says, "Hey I need you." Too much synthetic fertilizers inform the plant that an abundance of nutrition is available and the services of the mycorrhizal fungi are no longer needed. The chemical signalling is shut down and the fungi disconnect. In so doing the plant now has a far limited root absorption infrastructure and has become totally dependent on regular feeding program by the gardener, landscaper or farmer. It is also now further vulnerable to pathogens [soil & air borne] since the regulatory mechanisms and chemical inducer network provided by the fungi are no longer available to trigger alerts ahead of time. This works in the agro-chemical company's favour because a host of other chemicals like herbicides, fungicides and insecticides [in general more Pesticides period] must be employed to compensate for the loss of the fully functioning plant immune system. Basically your plant is now on life support and dependent on you more than ever now. Bottom line, inputs go up and profits go down. It just depends on how much a person is willing to learn and manage their program to the most sustainable outcome potential possible.

Real quick, I'll just stop here with one further easy to understand reference and not burden you with any more material than can be absorbed.
Some Easy to understand References
This was a great reference with easy to understand terminology and illustrations. It apparently was created by Dr Gary Harman when he was with Cornell Iniversity and BioWorks, Inc., Geneva, New York
Myths and Dogmas of Biocontrol - Gary Harman
Trichoderma - Frequently Asked Questions (FAQ) 
Trichoderma virens, a Plant Beneficial Fungus, Enhances Biomass Production and Promotes
 Growth through an Auxin-Dependent Mechanism in Arabidopsis Lateral Root

Tuesday, November 24, 2015

Soil Microbes use Rocket Science to Maintain the Earth's Atmosphere

One could also say that we could use the incredible Rocket Science of these Microbes to save our planet and reverse the negative effects brought about by the misuse and abuse of scientific discovery
Photo Credit: Nicholas A. Tonelli

So why is the Science of Soil Ecology & Microbes rejected in favour of the Industrial version for Commercial Agriculture ???

There's an old Sci-Fi classic from 1956 called "Forbidden Planet" where the film’s setting is of a bleak landscape on some far away planet and the concept of space travel that was inspired by many of the inventions which came out of world War II and intrigued people about the future possibilities of where mankind's ever expanding knowledge could take them. The film starts out with a spaceship from Earth (which looked more like a flying saucer aliens would have invented and used) which carries a small rescue mission that lands on a planet called, Altair IV, where a radio message from Dr. Edward Morbius warns them away from landing on the planet because of some unknown mysterious danger. This Dr Morbius and his daughter Altaira are the only people left alive from the original scientific expedition. An ancient alien race called the Krell have been gone for thousands of years, but they've left behind an incredible infrastructure and library of their existence among which there is one device Morbius calls the “plastic educator.” The device can greatly expand human intelligence, but there is a price to pay for that increased knowledge. As the film continues, these new arrivals from Earth are about to find out just how costly that knowledge really is. That machine in the film more than anything was intriguing to me as a kid watching that flick in the early 1960s. What if they could really invent such a device ? I mean just  suppose for a moment that you could be hooked up to such an intelligence machine and all the collective information of the various scientific disciplines could be uploaded into your mind. You could get employment almost anywhere right ? But the knowledge is nothing if you don't really understand how to properly apply it. If you have a great lack of communication and social skills (even common sense), like most of our world's intellects, you'd be greatly handicapped in the understanding of how to properly apply that knowledge to the benefit of yourself and others around you. Interestingly this would require cooperation with others and how many intellects have the patience to deal with those they view as their inferiors ? The world's soil microbial community are different and operate with an incredible amount of programmed instinctive knowledge and accomplish important tasks with incredible efficiency. In fact it appears that the microbial community is nothing more than life self-perpetuating information strings running remarkably sophisticated complex nano-machines and science hasn't a clue as to how they do what they do for us. 

illustration:  Mattias Adolfsson
When left alone and unmolested from  irresponsible human activities, all of the microbial soil communities underneath the  Earth's various ecosystems operate in a sophisticated complex united Social Network of cooperation that humans could only dream of. And yet we are supposed to be superior to them as the top organism on the planet. We've been force fed that these things are the most primitive living organisms on Earth, at least that's what the official scientific narrative has told us in School and the textbooks. As time pants on to the end, we find that is not really true. In fact all of the Earth's supposedly higher lifeforms would all perish without them. Frankly, I don't know if I really want humans to gain much more understanding and knowledge of the natural world under the present system based on their past historical activity of abuses of further knowledge. Take the latest research on a certain specific microbe which is brilliant at operating the Earth's biochemical nitrogen cycling. Here is an opening brief description of the soil microbe as given by Microbe Wiki  
"Anaerobic ammonium oxidation (Anammox) is a significant component of the biogeochemical nitrogen cycle. The process was discovered when it was noticed that ammonium was being converted to dinitrogen in a fluidized-bed reactor system at a yeast factory nearly 20 years ago. An unusual characteristic of anammox metabolism is the production of the metabolic intermediate hydrazine, which is one of the strongest reducing agents known in biological systems. "It is used as rocket fuel and in the manufacture of explosives and pesticides."
(Source - Microbe Wiki)
The last line in red of the quote in that description really expresses how much I hope that Scientists never crack the code of how these microbes do what they do. Even if they at some future point in time exclaim that they have solved the puzzle, you can bet that it will  somehow always be incomplete and imperfect. The very idea that such knowledge would be acquired and put to use by the present  irresponsible world leadership is a frightening scenario to ponder. And yet despite this, a team of European scientists in the Netherlands found something very interesting about this Anammox  bacteria. Published earlier this year in Nature, the researchers tell how they have ascertained the structure of a molecular machine that performs chemical wizardry using rocket science. Here is a reprinted quote from Nature and Discovery [keep in mind some of this may be boring for many]:
"Anaerobic ammonium oxidation (anammox) has a major role in the Earth's nitrogen cycle and is used in energy-efficient wastewater treatment. This bacterial process combines nitrite and ammonium to form dinitrogen (N2) gas, and has been estimated to synthesize up to 50% of the dinitrogen gas emitted into our atmosphere from the oceans. Strikingly, the anammox process relies on the highly unusual, extremely reactive intermediate hydrazine, a compound also used as a rocket fuel because of its high reducing power. So far, the enzymatic mechanism by which hydrazine is synthesized is unknown. Here we report the 2.7 Å resolution crystal structure, as well as biophysical and spectroscopic studies, of a hydrazine synthase multiprotein complex isolated from the anammox organism Kuenenia stuttgartiensis. The structure shows an elongated dimer of heterotrimers, each of which has two unique c-type haem-containing active sites, as well as an interaction point for a redox partner. Furthermore, a system of tunnels connects these active sites. The crystal structure implies a two-step mechanism for hydrazine synthesis: a three-electron reduction of nitric oxide to hydroxylamine at the active site of the γ-subunit and its subsequent condensation with ammonia, yielding hydrazine in the active centre of the α-subunit. Our results provide the first, to our knowledge, detailed structural insight into the mechanism of biological hydrazine synthesis, which is of major significance for our understanding of the conversion of nitrogenous compounds in nature."
Dinitrogen gas (N2) is a tough nut to crack. The atoms pair up with a triple bond, very difficult for humans to break without a lot of heat and pressure. Fortunately, this makes it very inert for the atmosphere, but life needs to get at it to make amino acids, muscles, organs, and more. Nitrogenase enzymes in some microbes, such as soil bacteria, are able break apart the atoms at ambient temperatures (a secret agricultural chemists would love to learn). They then "fix" nitrogen into compounds such as ammonia (NH3) that can be utilized by plants and the animals that eat them. To have a nitrogen cycle, though, something has to return the N2 gas back to the atmosphere. That's the job of anammox bacteria.
"Most nitrogen on earth occurs as gaseous N2 (nitrogen oxidation number 0). To make nitrogen available for biochemical reactions, the inert N2 has to be converted to ammonia (oxidation number −III), which can then be assimilated to produce organic nitrogen compounds, or be oxidized to nitrite (oxidation number +III) or nitrate (+V). The reduction of nitrite in turn results in the regeneration of N2, thus closing the biological nitrogen cycle."
Let's take a look at the enzyme that does this, the "hydrazine synthase multiprotein complex." Rocket fuel; imagine! No wonder the scientific community was surprised. The formula for hydrazine is N2H4. It's commonly used to power thrusters on spacecraft, such as the Cassini Saturn orbiter and the New Horizons probe that went by Pluto recently. Obviously, the anammox bacteria must handle this highly reactive compound with great care. Here's their overview of the reaction sequence. Notice how the bacterium gets some added benefit from its chemistry lab:
"Our current understanding of the anammox reaction (equation (1)) is based on genomic, physiological and biochemical studies on the anammox bacterium K. stuttgartiensis. First, nitrite is reduced to nitric oxide (NO, equation (2)), which is then condensed with ammonium-derived ammonia (NH3) to yield hydrazine (N2H4, equation (3)). Hydrazine itself is a highly unusual metabolic intermediate, as it is extremely reactive and therefore toxic, and has a very low redox potential (E0′ = −750 mV). In the final step in the anammox process, it is oxidized to N2, yielding four electrons (equation (4)) that replenish those needed for nitrite reduction and hydrazine synthesis and are used to establish a proton-motive force across the membrane of the anammox organelle, the anammoxosome, driving ATP synthesis."
We've discussed ATP synthase before. It's that rotary engine in all life that runs on proton motive force. Here, we see that some of the protons needed for ATP synthesis come from the hydrazine reaction machine. Watch the cool video below which is 3:21 minutes in length.

What does the anammox enzyme look like? They say it has tunnels between the active sites. The "hydrazine synthase" module is "biochemically unique." Don't look for a common ancestor, in other words. It's part of a "tightly coupled multicomponent system" they determined when they lysed a cell and watched its reactivity plummet. Sounds like an irreducibly complex system.

The paper's diagrams of hydrazine synthase (HZS) show multiple protein domains joined in a "crescent-shaped dimer of heterotrimers" labeled alpha, beta, and gamma, constituted in pairs. The machine also contains multiple haem units (like those in hemoglobin, but unique) and "one zinc ion, as well as several calcium ions." Good thing those atoms are available in Earth's crust.

Part of the machine looks like a six-bladed propeller. Another part has seven blades. How does it work? Everything is coordinated to carefully transfer electrons around. This means that charge distributions are highly controlled for redox (reduction-oxidation) reactions (i.e., those that receive or donate electrons). The choice of adverbs shows that their eyes were lighting up at their first view of this amazing machine. Note how emotion seasons the jargon:
"Intriguingly, our crystal structure revealed a tunnel connecting the haem αI and γI sites (Fig. 3a). This tunnel branches off towards the surface of the protein approximately halfway between the haem sites, making them accessible to substrates from the solvent. Indeed, binding studies show that haem αI is accessible to xenon (Extended Data Fig. 4c). Interestingly, in-between the α- and γ-subunits, the tunnel is approached by a 15-amino-acid-long loop of the β-subunit (β245-260), placing the conserved βGlu253, which binds a magnesium ion, into the tunnel."
We would need to make another animation to show the machine in action, but here's a brief description of how it works. The two active sites, connected by a tunnel, appear to work in sequence. HZS gets electrons from cytochrome c, a well-known enzyme. The electrons enter the machine through one of the haem units, where a specifically-placed gamma unit adds protons. A "cluster of buried polar residues" transfers protons to the active center of the gamma subunit. A molecule named hydroxylamine (H3NO) diffuses into the active site, assisted by the beta subunit. It binds to another haem, which carefully positions it so that it is "bound in a tight, very hydrophobic pocket, so that there is little electrostatic shielding of the partial positive charge on the nitrogen." Ammonia then comes in to do a "nucleophilic attack" on the nitrogen of the molecule, yielding hydrazine. The hydrazine is then in position to escape via the tunnel branch leading to the surface. Once they determined this sequence, a light went on:
"Interestingly, the proposed scheme is analogous to the Raschig process used in industrial hydrazine synthesis. There, ammonia is oxidized to chloramine (NH2Cl, nitrogen oxidation number −I, like in hydroxylamine), which then undergoes comproportionation with another molecule of ammonia to yield hydrazine."
So here's something you can meditate on when you take in another breath. The nitrogen gas that comes into your lungs is a byproduct of an exquisitely designed, precision nanomachine that knows a lot about organic redox chemistry and safe handling of rocket fuel. This little machine, which also knows how to recycle and reuse all its parts in a sustainable "green" way, keeps the nitrogen in balance for the whole planet. Intriguing. Interesting. As Mr. Spock might say, fascinating.

The above post is reprinted from materials provided by Radboud University, Discovery Institute and Nature. Note: Some materials were edited for content and length.
(Source) - (Source) - (Source)

So where does Mankind go from here ?

Image: EocWatch
For the past few decades the focus has always seemed to be on the big oil companies like Exxon, Chevron, BP, and Shell who have been perceived as the main climate change culprits. It's understandable because they are such big exposed targets and we are all shackled to them in what they provide for us as what we consider today as a normal life. And yet people for the most part have totally ignored the same dirty irresponsible behaviour of industrial corporate agricultural giants such as Monsanto, DuPont, Dow Agro-Chemical, Bayer, Syngenta, and BASF. Funny, we don't hardly here from BASF because they mostly deal with other large corporate business interests, but they are huge. All of them came out of World War II making munitions and other explosives for both the Allies and Axis powers, so they have a history of being in the death business. We know that between 20-30 percent of all man-made green house gases in the atmosphere comes from the overuse and abuse of chemicals manufactured by industrial agriculture. These very chemicals should be restricted for manufacturing purposes and transportation, not for the Earth's soil. By dumping agricultural chemicals [synthetic fertilizers, insecticides, fungicides, herbicides] onto our soils, we disrupt nature’s delicate balance of water, soil and air cycling. As we've seen in the above research, soil organisms have been perpetually monitoring Earth's carbon cycling components for countless 1000s of years, now suddenly we have 150 years of supposed scientific enlightenment under our belt and the function of these sophisticated cycling mechanisms are in jeopardy.

But what really are the true solutions for turning things around ? This just question begs once again, why is a scientific microbiological approach to farming practices considered, "anti-science" or "pseudo-science" by the Elite powerful and why are the people who advocate and practice such disciplines considered Voodoo Science practicing Luddites ??? You can thank the WSU Garden Professors for that one. Then on the other hand there are innumerable clever memes out there on the Organics sites floating around the Internet which promise a brighter future if everyone would just become an activist and practice what their favourite organization's philosophy recommends as a viable sustainable practice. While I am all for doing things by means of a holistic responsible approach through the practice of Biomimicry [replicating what Nature does], I am also aware that the world's problems won't be fixed through another materialistic scientific innovation approach as a cure all for what ails the world. I read the headlines daily promising that if humans would only just support such and such ideology regarding building healthy soils, we could turn around this present climate change crisis. It will never happen. First it assumes that everyone around the planet will get on board with the idea and they won't. Secondly, everyone reading knows the world we all live in, the all too common daily terrorizing News headlines lately and the failure of any government to provide viable solutions for any lasting piece and security. The best I can offer from a personal practice perspective is pay attention individually to your own garden, urban landscape or commercial farm and share your experiences with neighbours and friends. 
To conclude, here is a video of Dr. Kristine Nichols of the Rodale Institute talks about soil health and soil biology in regenerative organic systems. She hasn't always worked with Rodale, in fact she has worked as a Soil Microbiologist with the USDA, Agricultural Research Service (ARS) Northern Great Plains Research Laboratory (NGPRL) in Mandan, ND for over seven years. Since 1993, Dr. Nichols has studied arbuscular mycorrhizal (AM) fungi – a plant-root symbiont. Her most recent work involves the investigation of glomalin – a substance produced by AM fungi. Glomalin contributes to nutrient cycling by protecting AM hyphae transporting nutrients from the soil to the plant and to soil structure and plant health by helping to form and stabilize soil aggregates. Dr. Nichols has been examining the impacts of management such as crop rotation, tillage practices, organic production, cover crops, and livestock grazing on soil aggregation, water relationships, and glomalin. This comes from her Bio there. One of the main things I loved about her presentation here to farmers is the fact that she humbly acknowledges is how she and others as Scientists learn from the feedback from Farmers as to what works and what won't work or needs improving upon. That isn't normally done in today's world.

No references as I don't believe most are read anyways