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

1 comment:

  1. Great information, and I can tell you are trying to help the planet. I worry that I need a little more education to fully understand it.


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