How much energy do you need for ATP synthesis? part I

The other day I was trying to write my thesis when I started to divagate about something I’ll probably talk later in another post. Anyway, a paper took me to others papers and I ended up reading two papers about bioenergetics in archaea and bacteria that are really interesting if you are interested in such things. Also they help you to understand certain things about biodigesters!

So, I’m sharing some things I learned from them with you because I think it is important for us to know at least the basics of bioenergetics and also because I’m lonely here and I don’t have anyone to discuss about bioenergetics in anaerobes.

Ok, let’s start!

The paper I liked the most was “Adaptations of anaerobic archaea to life under extreme energy limitation” from Florian Mayer and Volker Müller, which explains about mechanisms for energy conservation in 4 different anaerobic archaea, and of course they discuss about methanogens. It has been about three years since it was confirmed that hydrogenotrophic pathways is actually cyclic but new things have been discovered and actually hydrogenotrophic methanogens are more versatile than we thought. But the reason of why I liked this review is not because of methanogens.

The interesting part is the introduction of some basic concepts of bioenergetics and also the description of the structure and functioning of the ATP synthase from archaea, which allows you to understand how this enzyme translocates H⁺ or Na⁺ and also how many of these are needed for the synthesis of ATP.

Anyway, what do you have to know to understand?

First, how much energy do you need for the synthesis of ATP from ADP and Pi?

According to Thauer et al. (1977) (Another review you should read):

So, for phosphorylation of ADP at standard conditions you need approximately +32 kJ/mol of energy. Now, where do you get such energy?

For that, two mechanisms of ATP synthesis are known: substrate level phosphorylation and che­miosmotic ion gradient-driven phosphorylation.

In the case of substrate level phosphorylation, there must be a highly exergonic reaction, which liberates enough energy to drive phosphorylation. In other words, the free energy (AG) of such reaction must be higher than -32 kJ/mol. The number of reactions that are that exergonic is limited, and some of them are listed in the review. The first three are the ones that are usually employed by fermentative organisms and they are reactions mediated by the enzymes acetate kinase, phosphoglycerate kinase and pyruvate kinase.

If you pay attention to those reactions, you will notice that there is something else they share besides their high free energies at standard conditions.

Anyway, for an anaerobic chemoorganotrophic organism fermenting hexoses to acetate, the maximum ATP gain is:

Yes, just 4 ATP. But the important thing you have to know from this is that for the gain of that number of ATP, the fermentative organism needs to produce hydrogen in order to recycle the reducing equivalents produced during fermentation (NADH, NADPH or ferredoxin). What would happen if, by any reason, they don’t get to produce the 4 molecules of hydrogen? I leave that question to you.

Now that it is clear that there are reactions whose free energies are high enough to drive ADP phosphorylation, let’s move on in to the second mechanism for ATP production: che­miosmotic ion gradient-driven phosphorylation.

We know that in this mechanism, ADP is phosphorylated by the activity of the ATP synthase and this reaction is driven by the ion gradient across the membrane (more outside, few inside). To maintain the ion gradient, the cell, mitochondria and chloroplasts must translocate ions across the membrane. And this, of course, requires energy. So, an exergonic reaction, which involves integral enzymes, is needed to couple ion translocation.

Electron transfer along integral enzymes/cytochromes (aka. the respiratory chain) is the classic example of exergonic reactions coupled to ion translocation. But of course, not all living organisms have respiratory chains. For this matter, such organisms must employ another type of reactions in order to obtain energy for ion translocation and a principal requisite is that those reactions must take place in the membrane.

The reaction of the CH₃-H₄M(S)PT:CH₃-CoM Methyl-tranferase in the methanogenic pathways along with hydrogen production by reduced ferredoxin are examples of reactions that couple ion translocation in organisms that don’t have cytochromes.

Now, this leads us to one of the most important questions: how much energy is needed in order to translocate one ion across the membrane?

This section is full of equations that explain how are you supposed to calculate the minimum amount of energy for the translocation of one ion across the membrane. Personally, I think that when you have to lead with equations, you are supposed to understand what those equations mean instead of memorizing them. So I’m not going to write any more equations (for that you can read the paper), instead, I’m going to try explaining them so that at least you can understand how the minimum energy for ion translocation is calculated.

In order to avoid any confusion, by using the word “ion” I’m referring to either H⁺ or Na⁺. Although H⁺ translocation is more common, organisms living under energy limitation use Na⁺. You’ll discover later in the paper why this information is important (specially you, Isco!).

Let’s start this long explanation by reminding you (again) that there must be an electrochemical ion gradient across the membrane and that this is possible thanks to exergonic reactions that keep pumping ions in order to maintain such gradient.

The electrochemical ion gradient is the one that defines the minimum of energy required.

Why? It’s really simple. Every system tries to reach the equilibrium. Since maintaining high concentrations of ions outside the membrane is going against such equilibrium, it obviously involves the input of energy. So imagine that you start with an “x” quantity of ions outside the membrane, which is higher than the one you find inside the membrane. For that quantity, you have to invest some “y” amount of energy in order keep translocating ions. After some time (and assuming ions are not returning to the inside of the membrane), you will have a greater amount of ions than the “x” initial quantity, which means you are far from reaching the equilibrium, so the energy required from ion translocation must be higher than the initial “y”. So the electrochemical ion gradient is just the difference of ion concentration across the membrane.

What I wrote above it’s what first equation of the article tries to explain with the appropriate concepts of thermodynamics. What do you need to know in order to calculate the electrochemical ion gradient? Well, first, the membrane potential. You can measure it directly or calculate its theoric value. Second, you need to know the concentrations of the ion outside and inside of the cell. Having at least that information will help you to determine the ion gradient.

As the article points it out, this value has been determined in just a few organisms and is about -180 to -200 mV. Now, you can calculate the minimum amount of energy required for translocation of only one ion, using the equation from the review:

In which:

, Represents the electrochemical ion gradient (-180 to -200 mV)

F, the Faraday constant (96. 485 KJ V^-1mol^-1)

n, the number of ions translocated (just 1)

If you substitute the values from above in the equation you’ll see that you need about -17 to -21 KJ/mol of energy in order to translocate just one ion across the membrane. However, the minimum energy could be lower if the electrochemical ion gradient is lower too. This is important because microorganisms that live under extreme energy limitations might use such strategy for their survival.

Now that we know the energy for the translocation of one ion across the membrane, the next question we have to answer is… how many ions do the cell need for the synthesis of ATP?

I’ll leave that question to you for now, because if I keep going with this post, it will be getting longer and longer and you will lose the interest.

I’ll try to write part two this week but meanwhile you can read the whole paper and try to answer that question. If you want to discuss something, you can ask me here or you can send me an email.

So, see you soon!

Absence of evolution? The Discover of  microorganism that has not evolved over millions of years.

The new discovery of two microbial biota in the deep waters of Turee Creek and Duck Creek in Western Australia, opens a new window on the early history of life,  to discover bacteria that can oxidize sulfur with a length of 2.3 billion years (2.3 Ga).

These bacteria were found permineralized in silica,  formed shortly after the great oxidation (2.4 to 2.2 Ga)  so these two biota can get an answer to what happened in the Precambrian era where increasing environmental oxygen caused an increase in the production of sulfate and nitrate metabolically usable.

But despite these two biota can provide information on the great oxidation on Earth  and how amazing is that comparing microbial morphology of fossil bacteria, also habitat and bacteria organization of "modern" sulfur found on the coast of Chile revealed that these two biota were exactly the same,  but with the news that the newly discovered had 2.3 Ga.

Similarities in their habitat

Fig. 1. Fabric biota from the Precambrian era. (A-C) Duck Creek 1. 8 Ga; (D-F) Turee Creek 2.3 Ga (Schopf et al., 2015).

These ecosystems biota are characterized by the presence of large bacterial populations that have the ability to metabolize sulfur,  also by a low content of dissolved oxygen, in some parts of the subsurface of the community, is essentially zero.  Usually comprise two regions: an anoxic zone below the resting surface consisting similar to an interlaced network of randomly oriented long fabric and commonly microorganisms anaerobic filamentous ≤ 10 microns in diameter.

Similarities in morphology and physiology

Fig. 2. Morphological Comparison between "modern" bacteria with fossil bacteria obtained from Turee Creek (2.3 Ga) and Duck Creek (1.8 Ga) (Schopf et al., 2015).

The marked similarities in morphology microbial,  habitat and community organization Precambrian their modern counterparts bacteria show a great adaptation to its environment under the seabed,  which has remained essentially unchanged for billions of years.

But really seems incredible that life in this habitat has not changed for almost half of the history of the earth when we see that evolution is evident,  although the apparent stagnation of two billion years of duration of the mentioned ecosystems relating to the sulfur cycle,  is consistent with Darwinian hypothesis which states that if there is a change in the Physical-Biological environment of a well-adapted ecosystem,  all biotic components should remain unchanged, i.e., the key to biology is not evolve unless cause changes in the physical or biological environment.

If you want to know more: http://www.pnas.org/content/early/2015/01/27/1419241112.full.pdf+html?sid=7d2171ae-a42c-4401-9dde-79c5d274d96b

Methanogens in Mars?

Excitement over the Curiosity rover’s recently reported detection of a ‘spike’ in localized atmospheric methane – persisting over a couple of months – is well founded. It’s possible that this represents a very real clue to past or present life on Mars. Or rather, life in Mars. The great majority of methane that we find here on Earth (whether in the air or in subsurface deposits) has a biological origin. This methane is generated by methanogenesis, a metabolic process that seems to be confined to members of the domain Archaea.

There’s more than one chemical pathway for making methane, but the most obvious is the combination of carbon dioxide with molecular hydrogen, and that’s precisely the reaction that a slew of methanogenic archaea latch onto. Molecular hydrogen is a potent source of chemical energy, and other organisms such as sulfate-reducing bacteria also gobble it up. So where do they find that hydrogen?

Methanogens. Credit: Maryland Astrobiology Consortium, NASA, and STScI

One source is where rock and water sit together. Radioactivity from rocks laced with elements like uranium can break up water molecules (the process of radiolysis), and the geochemical process of serpentization also spits out molecular hydrogen in abundance. Active hydrothermal vent systems on ocean beds are one environment where hydrogen is readily made, and methanogenic organisms thrive there. Places like these are, in relative terms, packed with chemical energy that life can exploit, and does.

Now a new study by Lollar, Onstott, Lacrampe-Couloume & Ballentine reported in Nature (2014) suggests that the deep (5km) continental zones could indeed be a major producer of hydrogen. Specifically, the most ancient Precambrian continental subsurface (rock older than about 540 million years), could generate molecular hydrogen at a rate 40 to 250 times higher than previously thought – a production on par with that associated with the much younger marine lithosphere. This Precambrian material exists in about 70% of the Earth’s continental area, and could contain as much water as all surface rivers, swamps, and lakes.

The conclusion is that the global production of molecular hydrogen needs an upward revision and, most critically, at least half of that is coming from the deep, ancient continental subsurface – which is not dry, not inert, and seems to be filled with life.

Connecting the discoveries of methane on Mars could give us an idea of how the Earth was in its earliest stages. It could also give us a clue as to where to look to find microorganisms based on the known methanogens in Earth.

Microbial Battery: A New Possibility of Self-Recharging Devices

Today's energy needs are an issue that is gaining much boom, ways of generating energy these days are very wide, in this one there are ways that may seem very strange to us but the human mind doesn't apparently has limits is only a matter of reinventing what nature already does by itself.

Among the alternatives to generate electricity is common to mention solar, wind, hydro, biomass, geothermal, nuclear, microbial cells, between many others. However it is last one sounds a little familiar with a slight change, the use of microorganisms. Harnessing energy from microorganisms sounds illogical, it is difficult to imagine in the mind, How something we can't see with the naked eye can produce more electricity than a conventional alkaline battery? these microorganisms allow us to use the oxidizing power generated when oxidize organic matter.

The idea is not as present, there are registers since 1911, when the botanist Michael Cressé Potter carried out the first attempt to use microorganisms to produce electricity, demonstrating that the breakdown of organic compounds by microorganisms is accompanied by the release of electricity that saw influenced by factors such as temperature, nutrient concentration of the media and the number of active microorganisms inducing the electricity production in microbial cells with a range of 0.3 to 0.5 Volt.

Microbial battery: microorganisms are attached to the carbon filaments of the battery

These results have been the basis of much research that handle electrochemical and engineering aspects that have allowed the development of microbial batteries as an alternative energy that can purify wastewater and recover the energy contained in it, if we compare with alkaline fuel cells in the market that can generate about 1.5 to 12 V, one of these can contaminate near 175,000 liters of water, and contain toxic substances such as zinc, manganese, bismuth, copper and silver, which produce various alterations human health while the microbial cells offer an option for direct power generation from oxidized donor and recovery of electricity from domestic wastewater, caring for the environment.

Pollution by alkaline baterries

 In 2013, Xie Xing introduced a microbial battery (MB) with modifications that promises to be more successful. In their MB prototyp the anode is colonized by microorganisms that oxidize domestic wastewater or glucose releasing electrons to an external circuit. The electrons enter a reoxidable silver oxide electrode solid-state (cathode), where the O2 is reduced making limited energy recovery by a voltage loss in this reaction. The molecular oxygen is not introduced into the battery and the ion exchange membranes is avoided which allows a high conversion efficiency of 49% power. The key of this device is the use in cathode functioning as a rechargable battery, in the next figure we can observe the operation of the microbial battery.

Schematic of two-step energy generation process using microbial batteries

This new contribution is not only to consider replacing domestic batteries whether not as a new deployment strategy batteries in cell phones or computers. Who has dreamed of having an electronic device that doesn't discharge? I would be very happy with something and maybe missing a lot for that but this progress is very promising so I don't rule out the possibility.

A memorandum of understanding between West Virginia State University and Universidad Autónoma de Coahuila

On January 19th, our school had the honor of the visit of Dr. Brian Hemphill, President of West Virginia State University with his wife Dr. Marisela Rosas Hemphill, MC. Katherine McCarthy,  Vice President of Enrollment Management and Student Affairs and Dr. José Ulises Toledo, Managing Director of Research and Public Service. WVSU team along with M.C. Maria de Lourdes Froto Madariaga, Director of our school interacted with students of our school in an event organised by the school administration. They presented the objectives as well as the benefits of the agreement to be signed between UAdeC and WVSU.

Later in the evening the agreement was signed by Lic. Jose Blas Dávila Flores, Rector of our University and Dr. Brian Hemphill, President of WVSU in the presence of University officials, Faculty, Student representatives and students our school.

This agreement will offer a lot of opportunities to both students and faculty of both universities such as exchange visits, International mobility for students, research stays that can lead to research publications contributing to scientific knowledge.

We, the students appreciate the effort of both Universities to offer us a good formation and hope we make good use of this opportunity.

Dr. Brian O. Hemphill, President of WVSU, the first lady and
few past and present students of Bioremediation Lab.

It started when...

Biorem Lab students have been putting all their efforts to undergo advanced training, carry out part of their thesis and to pursue higher studies at West Virginia State University for the past five years with orientation of Dr. Nagamani.

Thanks to the achievements of all those involved, their efforts have transcended today by signing of MOU between UAdeC. and WVSU. As a student of the School of Biological Sciences I feel happy and grateful because for us, actual students,  this MOU means new opportunities for us, which definitely we not want to miss.

It all starts with something and most of students from Biorem were the ones who laid the first stone for this to take place. A video of the past activities of biorem students in collaboration from Professors of WVSU is linked below. We hope you enjoy, plan to participate in activities such as exchange programs and research stays that could help in our Academic and Professional formation.

Best wishes Isco

Best wishes to Isco for his trip today to Havana, Cuba for oral presentation of his paper on "Synergic effect of volatile fatty acids (≥C3) at different concentrations on methanogenesis"at XI Simposio Latinoamericano de Digestión Anaerobia at Havana, Cuba (24-27 November, 2014). We are confident that Isco will do justice to his work done at our lab and will also enrich his knowledge by way participation and sharing it with others at school on return. Our sincere thanks to Rector of our University and President and Members of the City Council of Matamoros for their support to Isco to participate and present his work at this International event focused on anaerobic digestion.

mcrA and its utility in monitoring biodigesters

Hard work and consistent efforts of Ale and Lili, coupled with work carried out by Lorena and the support of Dr. Ricardo Oropeza Navarro, Instituto de Biotecnologia of UNAM, Cuernavaca, Morelos has resulted in the recent acceptance of our manuscript for publication in Frontiers in Microbiology. Abstract cum full paper is available in the web page of the journal. 

mcrA - biorem - Ale, Lili et al paper - Front. Microbiol., 2014

Congrats to the young team of Ale, Lili and Lorena and thanks to Dr. Ricardo & Dra. Miriam. Hope this is first of the many for Ale, Lili and Lorena.

"The theory of everything", An amazing reality

What do you know about the genius Sthephen Hawking? Very little is understood about Hawking in America or Canada,” says Anthony McCarten, the film’s screenwriter. “Nine of 10 people think he’s American. Most people think he was born disabled. They don’t know he was married and has three kids. There’s a lot of news to break with this film.”

The theory of everything is a movie based in the book of his ex wife travelling to infinitive: my life with Stephen.

In this story is showed not just when he falls in love, there is also something of his terriblee disease, and his most amazing accoplishments. 

McCarrten, promises the movie is an excellent work, and says that when Hawking saw the completed film for the first time, he was crying.

If we want to learn more, we can begin to consider go to watch it!

https://www.sciencenews.org/article/theory-everything-reveals-stephen-hawkings-personal-side

Unrecognized marine microbes consume up to 90 percent of the methane in the deep sea that would otherwise escape.

Methane emissions from the oceans are largely controlled by a specific group of microorganisms, they can consume up to 90% of the methane that is generated in the deep-sea. When this methane is exploted, is generated the precipitation of authigenic carbonates. 

Recently, a group of researchers have discovered a previously-unrecognized biological sink for a potent greenhouse gas: methane-breathing microbes living within rocky mounds on the seafloor. By using methane, these rock-dwelling microbes remove large amounts of the greenhouse gas from the ocean before they escape into the atmosphere. The findings were published in Nature Communications this week. 

Methane-consuming microorganisms are known to live near cold seeps -- ocean floor areas where methane seepage naturally occurs -- as well as in thin layers of sediment on the surface of huge, rocky outcroppings of calcium carbonate surrounding seep sites. These tall structures are better known as foundations for coral and sponges and homes for rockfishes, clams, and crabs. Finding active methane-consuming microbes in the interior of carbonate rocks extends their known habitat and introduces a new ecological niche for key methane consumers. 

"Methane is a much more powerful greenhouse gas than carbon dioxide, so tracing its flow through the environment is really a priority for climate models and for understanding the carbon cycle," Caltech’s Victoria Orphan says in a university statement. Her team previously found that two microorganisms that survive without oxygen work together to consume methane using sulfate from seawater: single-celled creatures called anaerobic methanotrophs and their bacteria partners. Until now, this two-microbe system has only been observed oxidizing methane at seeps. 

“No one had really examined these rocks as living habitats before,” Andrew Thurber of Oregon State says in a news release. They were just assumed to be inactive, serving as passive recorders of methane oxidation over time. “This goes to show how the global methane process is still rather poorly understood.” 

Using manned and robotic submersibles, the team collected rock samples from active cold seeps as well as carbonate mounds that appeared to be dormant at three sites: the tectonic plate boundary near Costa Rica (right), Eel River basin off the coast of northwestern California, and Hydrate Ridge off the Oregon coast (above). The rocks range in depth from 600 to 800 meters below the surface and in size from small pebbles to carbonate pavements stretching for dozens of kilometers. 

Back at the surface, the carbonates were cracked, and a series of tests confirmed that the rocks did indeed host anaerobic methanotrophs and sulfate-reducing bacteria. Genetic analysis showed how they were related to methane-munchers previously characterized in seafloor sediment. 

"The carbonate-based microbes breathed methane at roughly one-third the rate of those gathered from sediments near active seep sites," Caltech’s Jeffrey Marlow explains. The team used radiolabeled carbon-14 methane tracer gas to quantify the rates of methane consumption. "However, because there are likely many more microbes living in carbonate mounds than in sediments, their contributions to methane removal from the environment may be more significant."

Carbonate rocks can rise more than a hundred meters above the seafloor at methane seep sites like this one at Hydrate Ridge, Oregon.