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Intelligent Design, the best explanation of Origins

This is my personal virtual library, where i collect information, which leads in my view to Intelligent Design as the best explanation of the origin of the physical Universe, life, and biodiversity


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Intelligent Design, the best explanation of Origins » Photosynthesis, Protozoans,Plants and Bacterias » Anammox bacterias

Anammox bacterias

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1Anammox bacterias Empty Anammox bacterias on Fri Mar 14, 2014 11:32 am

Otangelo


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http://informahealthcare.com/doi/pdf...09230902722783

Mike S. M. Jetten1,2, Laura van Niftrik1, Marc Strous1, Boran Kartal1, Jan T. Keltjens1, and
Huub J. M. Op den Camp1
1Department of Microbiology, IWWR, Faculty of Science, Radboud University of Nijmegen, Toernooiveld 1, NL-6525
ED Nijmegen, The Netherlands, and 2Department of Biotechnology, Delft University of Technology, Julianalaan 67,
NL-2628 BC Delft, The Netherlands

Abstract (Enitre article is available to read)

Anaerobic ammonium-oxidizing (anammox) bacteria are one of the latest additions to the biogeochemical
nitrogen cycle. These bacteria derive their energy for growth from the conversion of ammonium and nitrite
into dinitrogen gas in the complete absence of oxygen. These slowly growing microorganisms belong to
the order Brocadiales and are affiliated to the Planctomycetes. Anammox bacteria are characterized by a
compartmentalized cell architecture featuring a central cell compartment, the “anammoxosome”. Thus far
unique “ladderane” lipid molecules have been identified as part of their membrane systems surrounding
the different cellular compartments. Nitrogen formation seems to involve the intermediary formation of
hydrazine, a very reactive and toxic compound. The genome of the anammox bacterium Kuenenia stuttgartiensis
was assembled from a complex microbial community grown in a sequencing batch reactor (74%
enriched in this bacterium) using a metagenomics approach. The assembled genome allowed the in silico
reconstruction of the anammox metabolism and identification of genes most likely involved in the process.
The present anammox pathway is the only one consistent with the available experimental data, thermodynamically
and biochemically feasible, and consistent with Ockham’s razor: it invokes minimum biochemical
novelty and requires the fewest number of biochemical reactions.
The worldwide presence of anammox
bacteria has now been established in many oxygen-limited marine and freshwater systems, including
oceans, seas, estuaries, marshes, rivers and large lakes. In the marine environment over 50% of the N2 gas
released may be produced by anammox bacteria. Application of the anammox process offers an attractive
alternative to current wastewater treatment systems for the removal of ammonia-nitrogen. Currently, at
least five full scale reactor systems are operational.

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2Anammox bacterias Empty Re: Anammox bacterias on Fri Mar 14, 2014 11:33 am

Otangelo


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Newly discovered bacterial partnership changes ocean chemistry

In a discovery that further demonstrates just how unexpected and unusual nature can be, scientists have found two strains of bacteria whose symbiotic relationship is unlike anything seen before.

Long, thin, hairlike Thioploca (meaning “sulfur braids” in Spanish) trichomes form chains down into marine sediment, which tiny anammox cells ride down like an elevator. At the bottom, the anammox cells consume nitrite and ammonium, or “fixed” nitrogen, the waste products of the Thioploca.

Nitrogen is a crucial building block of life, a prerequisite for photosynthesis. While nitrogen is present in abundance in the Earth’s atmosphere, to be useful for most living organisms, the nonreactive atmospheric nitrogen that diffuses into the ocean from the air must be converted into the biologically available “fixed” forms ammonium, nitrate and nitrite by specialized organisms called nitrogen fixers. Other organisms use up this fixed nitrogen and convert it back to di-nitrogen gas.

Living together in the mud beneath areas of high plant productivity, Thioploca and anammox intensify this part of the nitrogen cycle.

Gliding down through the mud, Thioploca chains bring down nitrate — a highly desirable resource in the harsh environment of oxygen-free sediments. As Thioploca encounters sulfide (which is a roadblock for most other bacteria) formed from the reaction of organic matter from above and sea water sulfate, it helps react nitrate with sulfide, producing nitrite and ammonium, which the anammox consumes and churns out di-nitrogen gas.

The anammox cells ride on Thioploca, living off its waste, and so both microbes thrive where others perish. Overall, however, they lock up an important resource for life in the ocean, making it unusable by the organisms at the base of the food chain that rely on photosynthesis to survive.

“The symbiotic relationship we discovered is an incredibly elegant chemical tandem between two chemolithotrophs — organisms which derive their metabolic energy purely from inorganic chemistry. We first predicted the symbiosis based on realization that Thioploca’s waste [nitrite and ammonium] are ‘bread and butter’ for anammox,” said Maria Prokopenko, lead author of a paper on the research that appeared in Nature earlier this month. “The prediction was confirmed by our team, proving that the symbiotic pair builds a very efficient natural ‘waste-treatment plant’ — destroying substantial quantities of fixed nitrogen while linking sulfur and nitrogen cycles in oxygen-free sediments.”

Prokopenko is currently a visiting scholar at Pomona College, but completed the research while she was a research assistant professor at USC, working with William Berelson, chair of the Earth Sciences Department at the USC Dornsife College of Letters, Arts and Sciences.

Prokopenko and Berelson collaborated with researchers from the University of California, Davis; the University of Southern Denmark; Pomona College; the University of Connecticut; Princeton University and the University of Cincinnati.

The symbiosis between Thioploca and anammox is not one creating widespread change throughout the ocean, but rather one that creates localized zones where fixed nitrogen is depleted faster than most expected.

Most of the samples collected were found off the coast of Baja California.

“As important as nitrogen is to life on this planet, it is amazing that we can discover new pathways and chemical reactions and biological partnerships involving this compound,” Berelson said.

Prokopenko, Berelson and others are presently studying nitrogen cycling in waters off Chile and Peru and are also investigating the history of nitrate preserved in ancient rocks.

The research was funded by the National Science Foundation (grant number OCE-0727123).

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3Anammox bacterias Empty Re: Anammox bacterias on Sun Aug 16, 2020 7:48 pm

Otangelo


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Anammox and Its Rocket Chemistry
Bacteria are often seen as rudimentary forms of life. But one look at their molecular structure is enough to convince us otherwise. Bacteria are extremely sophisticated, fully equipped with many exquisite molecular machines. One very strange group of bacteria discovered in the early 1990s, called anammox, provides a great example of the high-tech characteristics of bacteria. According to Laura van Niftrik and Mike Jetten, anammox bacteria are found in a wide variety of environments, including low-oxygen marine zones, treatment plant wastewater, coastal sediments, and lakes. It turns out that these bacteria are crucial to life on Earth: It is estimated they contribute up to fifty percent of N2 production from marine environments, resulting in the removal of fixed nitrogen. When discovered, anammox bacteria caused a real scientific stir. They are major players in Earth’s biogeochemical nitrogen cycle, and scientists wondered how such simple bacteria could perform a reaction previously considered impossible. Anammox converts NH3 and NO2 - into N2 under anaerobic conditions, that is, in the absence of O2. That is where it got its name: ANaerobic AMMonium OXidation.  “Anammox bacteria do not conform to the typical characteristics of bacteria but instead share features with all three domains of life, Bacteria, Archaea, and Eukarya, making them extremely interesting from an evolutionary perspective.” I would go further and say that the existence of these crucial and unusual bacteria is in fact extremely difficult to explain from an evolutionary perspective. How does an anammox bacterium fulfill its indispensable mission of replenishing nitrogen? It uses rocket science and some highly sophisticated organic synthesis skills.

The bacterium has an internal organelle covered by a double-layer membrane, not at all peculiar in prokaryotic cells. The greatest surprise was what was inside the organelle. Inside, scientists found hydrazine, which has a variety of uses, including for rocket fuel! Anammox somehow makes, stores, and uses a highly toxic, corrosive, and explosive liquid. Can you imagine a creature evolving one step at a time to store this stuff inside itself? Imagine trying to synthesize pure hydrazine by trial and error inside a bacterium. It wouldn’t take long to kill it! How would a bacterium evolve a hydrazine synthesis protocol without all the machinery to safely hold and use hydrazine? Is it plausible that a bacterium gained the ability to use pure, toxic, and explosive hydrazine by a step-by-step process that has no way to predict the future advantages of the poison? Why would a proto-anammox bacterium, which had previously not used hydrazine, and survived just fine without it, risk its life to evolve the ability to produce and store hydrazine, before it would do it any good? Another surprise is that anammox bacteria store hydrazine in internal compartments called anammoxosomes. Obviously, anammox bacteria must handle this explosive molecule with the greatest care. Chemical and microscopic analysis of the anammoxosome double-layer membrane, which encloses the hydrazine, revealed another surprise: The membrane consists of unique and bizarre lipids made from “ladderanes.” These are highly sophisticated chemical structures that many synthetic chemists would not even attempt to make. A typical ladderane is pentacycloanammoxic acid, which is composed of five fused rings of cyclobutane. It resembles a ladder and contains concatenated square ring structures formed by fused four-carbon rings. Concatenated four-membered rings are one of the hardest to make because kinetics and thermodynamics work against them. But anammox bacteria seem to have skipped organic synthesis classes and gone ahead and built them anyway. But why go to all the effort? It appears that anammox bacteria did it only to use hydrazine as an agent to convert NH3 and NO2 - into N2 in the absence of O2. So why would a bacterium synthesize N2, an almost inert gas that is practically useless for life as such? Anammox bacteria live all over the world. They are abundant in the oceans. They undertake this nearly impossible task simply to produce N2. 

But because of this “charity effort,” they regulate the N2 cycle and maintain the O2/N2 ratio of the Earth’s atmosphere.11 This little nanomolecular machine keeps the N2 at the balance needed for all life forms on our planet to survive. In essence, this little microbe uses rocket science12 to make life on earth possible, and sustainable. And we’re only beginning to understand this extraordinary bacterium. The enzymatic mechanism that makes hydrazine must also be incredible. “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.” The authors of the Nature paper go on to note a striking parallel: “Interestingly, the proposed scheme is analogous to the Raschig process used in industrial hydrazine synthesis.” So, again we find that another of our carefully planned inventions is only following in nature’s footsteps. The N2 gas that pairs with O2 in our atmosphere and is essential for life on Earth is, as another article puts it, “a byproduct of an exquisitely designed, precision nanomachine that knows a lot about organic redox chemistry and safe handling of rocket fuel.” The world of microbes proves more sophisticated with every discovery, manifesting more and more “surprises”—that is, evidence of foresight. Recently, we discovered another microbial wonder: the enigmatic comammox, or “complete ammonia oxidizer.” This bacterium can be found almost everywhere and does an even more spectacular job than anammox. Comammox perform complete nitrification on their own, a milestone of microbiology. Two different classes of nitrifier microbes have long been known to cooperate in carrying out the nitrification process where NH3 is oxidized to NO2 -, which is subsequently oxidized to NO3 -. But the comammox doesn’t share labor in nitrification. It catalyzes both nitrification steps, doing complete ammonia oxidation and thus conserving energy. It is difficult to escape the implications of all this: The need to sustain an atmosphere suited to life had to be anticipated from the start. And an array of microbes, equipped with a sophisticated arsenal of chemicals and capacities, had to be provided to meet that need.

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