The finely tuned and regulated carbon cycle, essential for life
http://reasonandscience.heavenforum.org/t2464-the-finely-tuned-carbon-cycle-essential-for-life
Carbon is present in all known life forms. It can be found dissolved in all water bodies on the planet. It is abundant in the Sun, stars, comets, meteorites, and in the atmospheres of most planets. Earth was just geology and chemistry – no biology. Then something happened to spark life, something mysterious. Between the geochemical origins of Earth and its eventual biological life is something scientists call a ‘black box’ – a figurative box they cannot peer into. Below the box are chemicals, above it DNA. The link is carbon, scientists agree, but how it happened precisely remains a mystery. The carbon in the atmosphere, the oceans, the trees, the soils, us and everything else is constantly in motion, flowing in a giant circle from air to land and back to air again in an unending, closed loop. The Law of the Conservation of Matter says that in a closed system matter can neither be created or destroyed. It can only cycle and recycle. The Earth has been a closed system almost from its origin with only solar energy, an occasional electromagnetic pulse from the sun, and stray bits of asteroids and comets entering from space. What’s here now has always been here, including carbon whose total amount is essentially the same as it was when Earth formed 4.5 billion years ago.
And what carbon does is cycle, a process essential to life on Earth. It’s a carefully regulated process so that the planet can maintain critical balances. Call it the Goldilocks Principle: not too much carbon, not too little, but just the right amount. For instance, without CO2 and other greenhouse gases Earth would be a frozen ball of rock. With too many greenhouse gases, however, Earth would be like hothouse Venus. Just right means balancing between the two extremes, which helps to keep the planet’s temperature relatively stable. It’s like the thermostat in your house. If it gets too warm, the cycle works to cool things off and vice versa. Of course, the planet’s thermostat gets overwhelmed at times, resulting periods of rapid warming or cooling (think Ice Ages).
Carbon Compounds in Cells 13
Carbon has unique quantum properties that make it the backbone of all organic compounds. It cycles through the atmosphere and the biomass of living organisms through various biochemical pathways. Its used for simple sugars like monosaccharides ( Ribose deoxyribose (five-carbon backbones) - building blocks for nucleic acids ) , Short-Chain Carbohydrates ( oligosaccharides, like lactose, sucrose, maltose ) Complex Carbohydrates ( polysaccharides like starch, cellulose, glycogen, chitin ), Lipids like fatty acids, Triglycerides (Neutral Fats), Phospholipids, Sterols and Their Derivatives, Waxes, proteins, nucleotides and amino acids.
Goldilocks principle: Earth's continued habitability due to geologic cycles that act as climate control 9
Scientists have shown how geologic process regulates the amount of carbon dioxide in the atmosphere. Researchers have documented evidence suggesting that part of the reason that Earth has become neither sweltering like Venus nor frigid like Mars lies with a built-in atmospheric carbon dioxide regulator — the geologic cycles that churn up the planet’s rocky surface.
The men who first proposed in some detail the heterotrophic origin of life were Haldane (1928) and Oparin (1924). Haldane (1928) proposed that, in the absence of oxygen, U.V. acting on a mixture of carbon dioxide, ammonia, and water would yield a large variety of organic compounds, including amino acids and sugars. These compounds would have accumulated in the oceans until they reached the consistency of hot dilute soup. The first organisms were large molecules synthesized under the influence of sunlight and were capable of replication in this rich medium. By mutation and selection the first cell arose and then gradually evolved a photosynthetic capacity as the rich medium became used up. Photosynthesis led to the production of oxygen and thus accounted for the present level of oxygen in our atmosphere. This picture is the dominant view held today. The only modification was made by the experiments of Miller (1955), where the atmosphere was methane, ammonia, and hydrogen. The main problem which is left is the appearance of a molecule which is capable of self-reproduction. The best guess is that it was an RNA molecule (Crick, 1968; Orgel, 1968). This RNA molecule would then evolve by mutation and selection until it coupled with proteins by means of a primitive genetic code. The evolution of metabolism, anabolic and catabolic, is one of a gradual development of autotrophy from the initial heterotrophy, again by a process of mutation and selection as the soup became depleted (Horowitz, 1945).
Plate tectonics makes possible the carbon cycle, which is essential to our planet’s habitability. 10 This cycle is actually composed of a number of organic and inorganic subcycles, all occurring on different timescales. These cycles regulate the exchange of carbon-containing molecules among the atmosphere, ocean, and land. Photosynthesis, both by land plants and by phytoplankton near the ocean surface, is especially important, since its net effects are to draw carbon dioxide from the atmosphere and make organic matter. Zooplankton consume much of the organic matter produced in the sunlight-rich surface. The carbonate and silicate skeletons of the marine organisms settle obligingly on the ocean floor, to be eventually squirreled away beneath the continents.
MICROBIAL DECOMPOSERS: FUNDAMENTAL for the Earth's biogeochemical cycles 14
All living organisms depend on the supply of necessary elements from the Earth. Since the Earth is a closed system with a finite supply of essential elements such as hydrogen (H), oxygen (O), carbon (C), nitrogen (N), sulfur (S) and phosphorus (P), recycling of these elements is fundamental to avoid exhaustion.
Beside the Nitrogen cycle, silicon cycle, water cycle, Phosphorus, Iron, and Trace Mineral cycles , the global carbon cycle is essential for life on earth. How was it all setup ? Design, or a giant lucky accident ?!
Carbon is the fourth most abundant element in the universe, the fifteenth most abundant element on Earth, and the second most abundant in the human body after oxygen. 8 Carbon is present in all known life forms. It can be found dissolved in all water bodies on the planet. It is abundant in the Sun, stars, comets, meteorites, and in the atmospheres of most planets. Carbon is star dust. It first formed in the interiors of stars not long after the Big Bang and then scattered into space as dust as a result of supernova explosions. Over time, it coalesced into star systems such as ours, as well as planets, comets, and other heavenly bodies. Eventually, it coalesced into us. Carbon is life. It exists in every organic life form. Life is impossible without it.
Carbon Compounds in Cells 13
Carbon has unique quantum properties that make it the backbone of all organic compounds. It cycles through the atmosphere and the biomass of living organisms through various biochemical pathways. Its used for simple sugars like monosaccharides ( Ribose deoxyribose (five-carbon backbones) - building blocks for nucleic acids ) , Short-Chain Carbohydrates ( oligosaccharides, like lactose, sucrose, maltose ) Complex Carbohydrates ( polysaccharides like starch, cellulose, glycogen, chitin ), Lipids like fatty acids, Triglycerides (Neutral Fats), Phospholipids, Sterols and Their Derivatives, Waxes, proteins, nucleotides and amino acids.
When combined with water it forms sugars, fats, alcohols, fats, and terpenes. When combined with nitrogen and sulfur it forms amino acids, antibiotics, and alkaloids. With the addition of phosphorus, it forms DNA and RNA – the essential codes of life – as well as ATP, the critical energy-transfer molecule found in all living cells. The carbon atom is the essential building block of life. Every part of your body is made up of chains of carbon atoms, which is why we are known as “carbon-based life forms.” We are star dust.
Carbon is a miracle. Chemically, we’re just a bunch of inert compounds. What breathes life into us? The answer is the relationship between the molecules of energy and nutrients fueled by carbon and water. Billions of years ago, Earth was just geology and chemistry – no biology. Then something happened to spark life, something mysterious. Between the geochemical origins of Earth and its eventual biological life is something scientists call a ‘black box’ – a figurative box they cannot peer into. Below the box are chemicals, above it DNA. The link is carbon, scientists agree, but how it happened precisely remains a mystery. The carbon in the atmosphere, the oceans, the trees, the soils, us and everything else is constantly in motion, flowing in a giant circle from air to land and back to air again in an unending, closed loop. The Law of the Conservation of Matter says that in a closed system matter can neither be created or destroyed. It can only cycle and recycle. The Earth has been a closed system almost from its origin with only solar energy, an occasional electromagnetic pulse from the sun, and stray bits of asteroids and comets entering from space. What’s here now has always been here, including carbon whose total amount is essentially the same as it was when Earth formed 4.5 billion years ago.
And what carbon does is cycle, a process essential to life on Earth. It’s a carefully regulated process so that the planet can maintain critical balances. Call it the Goldilocks Principle: not too much carbon, not too little, but just the right amount. For instance, without CO2 and other greenhouse gases Earth would be a frozen ball of rock. With too many greenhouse gases, however, Earth would be like hothouse Venus. Just right means balancing between the two extremes, which helps to keep the planet’s temperature relatively stable. It’s like the thermostat in your house. If it gets too warm, the cycle works to cool things off and vice versa. Of course, the planet’s thermostat gets overwhelmed at times, resulting periods of rapid warming or cooling (think Ice Ages).
Goldilocks principle: Earth's continued habitability due to geologic cycles that act as climate control 9
Scientists have shown how geologic process regulates the amount of carbon dioxide in the atmosphere. Researchers have documented evidence suggesting that part of the reason that Earth has become neither sweltering like Venus nor frigid like Mars lies with a built-in atmospheric carbon dioxide regulator — the geologic cycles that churn up the planet’s rocky surface.
Scientists have long known that “fresh” rock pushed to the surface via mountain formation effectively acts as a kind of sponge, soaking up the greenhouse gas CO2. Left unchecked, however, that process would simply deplete atmospheric CO2 levels to a point that would plunge Earth into an eternal winter within a few million years during the formation of large mountain ranges like the Himalayas — which has clearly not happened.
And while volcanoes have long been pointed to as a source of carbon dioxide, alone they cannot balance out the excess uptake of carbon dioxide by large mountain ranges. Instead, it turns out that “fresh” rock exposed by uplift also emits carbon through a chemical weathering process, which replenishes the atmospheric carbon dioxide at a comparable rate.
Fortunately, the miraculous carbon cycles keeps working, scrubbing excess CO2 out of the atmosphere or adding more if necessary. Who does all this regulatory work? green, growing plants and. Photosynthesis is the process by which carbon is transferred from sky to soil. It’s what makes the Goldilocks principle tick. It keeps the Goldilocks principle ticking over time – long periods of time. The two work in concert. The greenhouse effects of an excessive build up of CO2 in the atmosphere, for instance, will impact the fate of generations of living things. Carbon and life interact and adjust to each other, regulating and responding in a sophisticated dance. Carbon chooses the music, if you will, while evolution dictates the steps in a planetwide choreography. It is a dance with a profound effect on audience members.
Carbon is not the only dance on the planet, of course. Our world is full of cycles – water, energy, nutrients, nitrogen, phosphorus, and many more – interacting with each other in complicated ways. Carbon has both. Its short, or fast, cycle revolves around green plants and photosynthesis – the process by which carbon is separated from oxygen, stored in roots and soils, and released back into the atmosphere via death and decomposition.
The process by which atmospheric CO2 gets converted into soil carbon requires is sunlight, green plants, water, nutrients, and soil microbes. There are four basic steps to the CO2 / soil carbon cycle:
Photosynthesis: This is the process by which energy in sunlight is transformed into biochemical energy in the form of a simple sugar called glucose via green plants – which use CO2 from the air and water from the soil, releasing oxygen as a by-product. The chemical reaction looks like this: CO2 + H2O + energy = CH2O + O2
Resynthesis: Through a complex sequence of chemical reactions, glucose is resynthesized into a wide variety of carbon compounds, including carbohydrates (such as cellulose and starch), proteins, organic acids, waxes, and oils (including hydrocarbons), all of which serve as ‘fuel’ for life on Earth.
Exudation: Carbon created by photosynthesis can be exuded directly into soil by plant roots to nurture microbes and other organisms. This process is essential to the creation of soil from the lifeless mineral soil produced by the weathering of rocks over time. The amount of increase in organic carbon is governed by the volume of plant roots per unit of soil and their rate of growth. More active green leaves mean more roots, which mean more carbon exuded.
Humification: or the creation of humus – a chemically stable type of organic matter composed of large, complex molecules made up of carbon, nitrogen, minerals, and soil particles. Visually, humus is the dark, rich layer of topsoil that people generally associate with stable wetlands, healthy rangelands, and productive farmland. Once carbon is stored as humus it has a high resistance to decomposition, and therefore can remain intact and stable for hundreds or thousands of years.
Let’s follow three carbon molecules from the air to three separate destinations. Imagine these molecules enjoying a carefree life as a gas, each accompanied by two oxygen molecules, as they joyride side-by-side through the air without a care in the world. Suddenly, all three smack into a green, leafy something and quickly pass from the bright light of the atmosphere into the dark, vascular world of a plant. Now their carefree existence turns into a wild toboggan ride of photosynthesis. The three molecules go through a series of transformative twists, turns, and drops as they travel through the plant, bathed in green, drenched in water, stripped of their oxygen buddies, and eventually picking up new molecular passengers, including hydrogen, nitrogen, and more carbon. At the end of their wild ride, the molecules are no longer part of a gas having become instead part of a sugary carbohydrate called glucose, a vital source of energy for the plant. At this point a new ride begins and our three carbon molecules are quickly sent in three separate directions. The first molecule concludes its journey in a leaf cell, where the glucose is converted by the plant into a kind of biological battery called starch which it stores for later use, such as winter when photosynthesis is turned off. Other uses of glucose by the plant include respiration, creating the sweetness in fruit, conversion into cellulose for cell-wall strengthening, forming fatty lipids for storage in seeds, and generating proteins, which are an important source of food for all living things. In this case, our carbon molecule rests quietly in its cell waiting to be summoned when the leaf is suddenly ripped from its host by a hungry herbivore. After a brief but tumultuous ride through grinding teeth, the molecule slides downward into a smelly stomach and eventually passes into the animal’s digestive tract, where the starch is processed and the carbon absorbed into a cell of muscle tissue. A month later, the cycle is completed when the animal breaks a leg and dies in the wild. As it decomposes, the carbon molecule is exposed to the air where it picks up two oxygen atoms swinging by and together they rise upward to begin the joyride all over again.
The second carbon molecule shoots underground through the plant’s stem and then slows to a crawl as it reaches the tip of a slender root. The plant intends to use the glucose to build new root mass so it can tap additional water and nutrients, but before it can the plant suddenly shudders as half of its leaves are wrenched away by the hungry herbivore. This causes the plant to send an emergency signal to its roots: retreat! To help recover its vigor and grow new leaves again, the plant must now use the glucose stored in its root cellar, ordering the supplies upward. It’s not a crisis however (unless the hungry herbivore comes back around for a second bite) because by removing last year’s dead material along with this year’s green growth, the herbivore has freed up the plant to grow unimpeded. One of the plant’s first responses is to slough off the tips of its roots to conserve energy. That means our second carbon molecule finds itself detached and isolated from the rest of the plant, lost and lonely in the soil – but not for long. Soon, the decaying root tips attract the attention of a host of hungry microbes and other critters, including protozoa, nematodes, fungi, earthworms, arthropods, and a huge variety of bacteria (there are more microbes in a teaspoon of soil than humans on the planet). Bacteria go to work first. These are single-celled creatures with one goal in mind: eat! They are particularly ravenous for carbon and after they have digested a bunch of it they become attractive to predatory critters in the neighborhood. Soon, a feeding frenzy begins. Our particular carbon molecule disappears down the throat of a nematode, which is a type of tiny worm. There are approximately one million different species of nematodes on the planet, found in every type of ecosystem, accounting for 80 percent of all creatures in existence on Earth. That makes for a lot of eating and pooping going on below ground.
In this case, the nematode eventually excretes our molecule into the soil where it bonds with two sly oxygen molecules hanging out (smoking cigarettes) in the tiny air pockets between soil particles and becomes part of a carbon dioxide molecule once again. Eventually this new CO2 molecule makes its way up to the soil surface and back into the atmosphere – a process scientists call soil respiration – to join zillions of their buddies for another wild ride. Round and round. Meanwhile, our third carbon molecule has followed a similar path to the plant’s roots, only to end up inside a fungus instead of a nematode – and not just any fungus, but one of the heroic mycorrhizal varieties. These are long, skinny filaments that live on the surface of plant 17 roots with which they share a symbiotic relationship, trading essential nutrients and minerals back and forth (mycorrhiza is Greek for fungus + root, or “I’ll scratch your carbon if you’ll scratch mine”). The fungus-root mutualism reduces a plant’s susceptibility to disease while and increasing its tolerance to adverse conditions, including prolonged drought spells or salty soils. Fungi in general are best known to humans as the source of mushrooms, yeasts, and the molds that make cheeses tasty, ruin houses in humid climates, and produce antibiotics. Like plants and animals, fungi form their own taxonomic kingdom. In fact, there are an estimated two to five million individual species of fungi on the planet, of which less than 5% have been formally classified by taxonomists. In the soil, fungi can be “good guys” or “bad guys” depending on your perspective (the “bad guys” cause a variety of diseases). Our third carbon molecule ends up in a good guy called an arbuscular mycorrhizal fungus. After absorbing the bit of glucose containing our molecule from the plant root, the skinny arbuscular fungus next pushes the carbon into one of its hyphae – hair-like projections that extend as much as two inches into the soil in a never-ending search for nutrients. Then, in a process that is not completely understood by scientists the carbon molecule is extruded into the soil from the hyphae in a sticky protein called glomalin – one of nature’s superglues. You can feel glomalin. It’s what gives soil its tilth – the rich, smooth texture that tells experienced farmers and gardeners that they holding great soil in their hands. To create tilth, the soil engine needs both biology and chemistry working together and glomalin is the glue that binds them. It’s an extraordinary process, one which creates a world of possibilities!
Identification of how and where carbon occurs within an environment is an important signal to know whether the setting is, or is capable of, hosting life. On Earth today, there are three major carbon-bearing reservoirs that are interrelated: the atmosphere; the hydrosphere; and the litosphere. Superimposed on these, and acting throughout, is the biosphere. 4 We now know that comet and asteroid dust deliver tons of organics to the Earth every day, therefore this flux of reduced carbon from space probably also played a role in making the Earth habitable. 3
In the speculations on the origin of life, the most difficult conceptual problems deal with the complexity of the first organism and the complexity of its environment. 7 There are four possibilities:
(I) the first organism was simple (e.g., RNA) and its environment was complex (heterotrophic origin);
(2) the organism was simple (e.g., clays) and its environment was simple (autotrophic origin);
(3) the organism was complex and its environment was complex (heterotrophic panspermia);
(4) the organism was complex and its environment was simple (autotrophic panspermia).
The men who first proposed in some detail the heterotrophic origin of life were Haldane (1928) and Oparin (1924). Haldane (1928) proposed that, in the absence of oxygen, U.V. acting on a mixture of carbon dioxide, ammonia, and water would yield a large variety of organic compounds, including amino acids and sugars. These compounds would have accumulated in the oceans until they reached the consistency of hot dilute soup. The first organisms were large molecules synthesized under the influence of sunlight and were capable of replication in this rich medium. By mutation and selection the first cell arose and then gradually evolved a photosynthetic capacity as the rich medium became used up. Photosynthesis led to the production of oxygen and thus accounted for the present level of oxygen in our atmosphere. This picture is the dominant view held today. The only modification was made by the experiments of Miller (1955), where the atmosphere was methane, ammonia, and hydrogen. The main problem which is left is the appearance of a molecule which is capable of self-reproduction. The best guess is that it was an RNA molecule (Crick, 1968; Orgel, 1968). This RNA molecule would then evolve by mutation and selection until it coupled with proteins by means of a primitive genetic code. The evolution of metabolism, anabolic and catabolic, is one of a gradual development of autotrophy from the initial heterotrophy, again by a process of mutation and selection as the soup became depleted (Horowitz, 1945).
The Carbon cycle 5
The carbon cycle is the biogeochemical cycle by which carbon is exchanged among the biosphere, pedosphere, geosphere, hydrosphere, and atmosphere of the Earth. Along with the nitrogen cycle and the water cycle, the carbon cycle comprises a sequence of events that are key to make the Earth capable of sustaining life; it describes the movement of carbon as it is recycled and reused throughout the biosphere, including carbon sinks.
Under terrestrial conditions, conversion of one element to another is very rare. Therefore, the amount of carbon on Earth is effectively constant. Thus, processes that use carbon must obtain it from somewhere and dispose of it somewhere else. The paths of carbon in the environment form the carbon cycle. For example, photosynthetic plants draw carbon dioxide from the atmosphere (or seawater) and build it into biomass, as in the Calvin cycle, a process of carbon fixation. Some of this biomass is eaten by animals, while some carbon is exhaled by animals as carbon dioxide. The carbon cycle is considerably more complicated than this short loop; for example, some carbon dioxide is dissolved in the oceans; if bacteria do not consume it, dead plant or animal matter may become petroleum or coal, which releases carbon when burned
Plants, fueled by the Sun’s radiation, convert CO2 to sugar and other carbohydrates by photosynthesis. 6 Organisms that consume plants derive their energy from the oxidation of those photosynthetic products. Further up the food chain, organisms that consume other consumers ultimately derive their energy from the same source. In these ways, the CO2 that had been taken out of the atmosphere and oceans by plants is returned from where it came; the process is called respiration. Integrated over all organisms and all environments, the loop between photosynthesis and respiration makes up the biological component of Earth’s carbon cycle.
Carbon-bearing reservoirs on Earth
Schematic representation of the pathways through which the carbon cycles operate on Earth today.
Evidence for the earliest existence of water comes from the oxygen isotopic composition of the mineral zircon present in meta-sediments from the Jack Hills Formation of Western Australia. Most of these grains are around 4.2 Gyr old, but there are some detrital zircons with ages as ancient as 4.4 Gyr and their presence implies the existence of a fairly widespread ocean, as well as reworked crustal sediments . Therefore, by 4.4 Gyr ago, Earth already had an atmosphere, a lithosphere and a hydrosphere, and the reservoirs were actively connected. Tectonic activity occurred, where crust was subducted and recycled, but plate tectonics was not completely established. At some point between the formation and 3.5 Gyr ago, Earth had stabilized to the extent that there were three dynamically interacting reservoirs: the atmosphere, the lithosphere and the hydrosphere; and plate tectonics was taking place with a mechanism of plate movement close to that which is in operation today.
The mechanism of photosynthesis acts to remove CO2 from the atmosphere and replenishes it with oxygen. This reaction is balanced by respiration, which removes O2 from the atmosphere and replaces with CO2. As the biomass of photosynthesizing organisms increased, there was an increasing ‘fixing’ of carbon by burial, as the micro-organisms lived and died, gradually increasing the oxygen content of Earth's atmosphere. At around 2.3 Gyr ago, the switch from a reducing to an oxidizing atmosphere became permanent, and the atmosphere had evolved to a composition closer to that observed today (Holland 2002). The unambiguous establishment of life can be tracked through the fossil record, with the first appearance of macro-fossils ca 600 Myr ago (e.g. Conway Morris 1993). Through time, variations in global climate, impacts and tectonic processes have changed the surface of the Earth, and species have evolved and become extinct. However, overall, since the biosphere became established and the atmosphere oxidizing, there have been no gross changes to the way in which the terrestrial carbon cycles have operated.
Plate tectonics makes possible the carbon cycle, which is essential to our planet’s habitability. 10 This cycle is actually composed of a number of organic and inorganic subcycles, all occurring on different timescales. These cycles regulate the exchange of carbon-containing molecules among the atmosphere, ocean, and land. Photosynthesis, both by land plants and by phytoplankton near the ocean surface, is especially important, since its net effects are to draw carbon dioxide from the atmosphere and make organic matter. Zooplankton consume much of the organic matter produced in the sunlight-rich surface. The carbonate and silicate skeletons of the marine organisms settle obligingly on the ocean floor, to be eventually squirreled away beneath the continents.
Plankton Revealed - A critical component of life on Earth 11
Plankton are an essential component of life on Earth. Marine plankton, found in all ocean ecosystems, play a critical role in maintaining the health and balance of the ocean and its complex food webs. The oxygen, nutrients, and biomass they produce also sustain terrestrial life—from the food we eat to the air we breathe. With 71% of the Earth covered by the ocean, phytoplankton are responsible for producing up to 50% of the oxygen we breathe. These microscopic organisms also cycle most of the Earth’s carbon dioxide between the ocean and atmosphere. Plankton also play a role at the end of the food web—as decomposers and detritivores. These plankton, including bacteria, fungi, and worms, break down and consume dead plant and animal material that falls through the water column as "marine snow." Marine snow often includes fecal matter, sand, soot, skin, and other organic and inorganic particles descending to the seafloor.
Without plankton, we as human beings would not be here; and without them, we’d probably disappear. So we’d better be aware of what happens to them, including what we do to them. 12 “These tiny living organisms, when they die, sediment at the bottom of the oceans. With time, the accumulated sediments generate different kinds of rocks like limestone, chalk and opal. We now find rock structures all over the world composed of billions of these microscopic organisms, such as the white cliffs of Dover in England, or the Sisquoc formation in Lompoc, Santa Barbara. Most of northern Europe is actually of planktonic origin.”
First, we have what we call the protists, mainly the phytoplankton, if you want. There are up to 10 million of them in every liter of seawater. Then we have the metazoans, like the zooplankton, which graze on the protists. We also have bacteria – up to 1 billion/liter – and viruses – up to 10 billion/liter. These viruses are not dangerous for human beings, only for the phytoplankton and the zooplankton. They have an important regulatory role because they maintain the turnover in the system. Nature does not tolerate excess, it likes equilibrium between species. This means that as soon as one species becomes dominant, nature finds a way to eliminate it.”
First, and this is probably the most obvious one, they are at the base of the food chain. They provide food to the fish which we eat. Second, they still generate half of the oxygen on the planet, removing CO2 from the atmosphere in the process. We know why this is so important: Carbon dioxide, being a greenhouse gas, is contributing to the global warming of the Earth. Hence the importance of reducing its presence in the atmosphere. “That forests are the first lung of our planet is well-known; what is much less known is that oceans constitute the second. It is like an invisible forest in the oceans,” says Bowler.
Also central to the carbon cycle is the chemical weathering of silicate rocks on the continents. This occurs when rainwater, made acidic with dissolved carbon dioxide from the atmosphere, dissolves minerals in exposed rock. The rivers eventually carry dissolved silica (SiO2), calcium, and bicarbonate ions (derived from the carbon dioxide) to the oceans. Phytoplankton and zooplankton—and to a lesser extent, corals and shellfish— then remove these dissolved chemicals from the ocean to build their silicate and calcium carbonate skeletons. The carbon cycle is completed when the subducted carbonates are pressure-cooked deep in the crust, releasing carbon dioxide that eventually finds its way to the surface through volcanoes and springs.
As an example, diatoms are the major phytoplankton group that play a role in maintaining oxygen levels in the atmosphere and in the carbon cycle that sustains primary production in aquatic environments. The most abundant diatom is Chaetocerus 15
Diatoms
Diatoms are one of the most important lifeforms on the planet. These single celled organisms have shells of silica and make almost half of all the organic compounds produced in the ocean. These are just a few of the reasons why plankton deserve the title “Earth’s most important creatures”. Plankton are responsible for 50% of earth’s oxygen. They are an essential part of the food chain. And billions of billions of ancient plankton have given their bodies to form the crude oil that powers modern society. Yet we rarely recognise their contribution to life on this planet, including our own.
No one really knows how many different diatoms are out there, but conservative estimates suggest around 100,000 to 200,000 species, making them among the most species-rich lineages of eukaryotes. 19
God’s micro world 17
Diatoms are marvels of complex architectural engineering. They have the unique ability to fashion intricate glass-houses for themselves by using the silica found naturally in sea-water. Not only are they intricately built, but they are found in all known geometrical shapes and are symmetrical in three dimensions, having perfectly matched tops and bottoms that are held together until the plant dies and the two halves come apart. Very rarely in biological systems do you find the use of straight lines for structural support. But diatoms are masters, not only at straight lines, but also at circles, triangles, squares, and ovals.
Diatoms have a sophisticated calcium and nitric oxide-based surveillance system for monitoring environmental stresses that can detect the release of aldehydes by its wounded neighbours. 18
The life of diatoms in the world’s oceans 16
More on How Microbes Make Earth Habitable
These Kaleidoscopic Masterpieces Are Invisible to the Naked Eye
The amazing diversity and beauty of Diatoms
MICROBIAL DECOMPOSERS: FUNDAMENTAL for the Earth's biogeochemical cycles 14
All living organisms depend on the supply of necessary elements from the Earth. Since the Earth is a closed system with a finite supply of essential elements such as hydrogen (H), oxygen (O), carbon (C), nitrogen (N), sulfur (S) and phosphorus (P), recycling of these elements is fundamental to avoid exhaustion. Microbes are critical in the process of breaking down and transforming dead organic material into forms that can be reused by other organisms. This is why the microbial enzyme systems involved are viewed as key ‘engines’ that drive the Earth's biogeochemical cycles.
The terrestrial carbon cycle is dominated by the balance between photosynthesis and respiration. Carbon is transferred from the atmosphere to soil via ‘carbon-fixing’ autotrophic organisms, mainly photosynthesising plants and also photo- and chemoautotrophic microbes,that synthesise atmospheric carbon dioxide (CO2) into organic material. Fixed carbon is then returned to the atmosphere by a variety of different pathways that account for the respiration of both autotrophic and heterotrophic organisms. The reverse route includes decomposition of organic material by ‘organic carbon-consuming’ heterotrophic microorganisms that utilise the carbon of either plant, animal or microbial origin as a substrate for metabolism, retaining some carbon in their biomass and releasing the rest as metabolites or as CO2 back to the atmosphere
Negative feedback loops maintain the whole cycle in balance. Perhaps the most important stabilizing feedback is the dependence of the rate of chemical weathering on temperature. Here’s how it works: Suppose a prolonged period of large volcanic eruptions rapidly increased the amount of carbon dioxide in the atmosphere. Through the greenhouse effect, the upsurge in carbon dioxide would raise the global temperature. The higher temperature and carbon dioxide level, in turn, would speed up chemical weathering, and thus the removal of carbon dioxide from the atmosphere. Eventually, the carbon dioxide and temperature would return to their preeruption levels. Conversely, a drop in carbon dioxide would slow chemical weathering, allowing carbon dioxide to build up in the atmosphere. In either case, the loop comes full circle. Thus, plate tectonics, together with plant life, makes a planet much more nurturing for all life.
The parallel biosphere of chemotrophy on Earth
Within only the past 30 years, an understanding of the biosphere has become possible that completely inverts the view that had been accreting for more than a century. A pivotal event in this reframing was the discovery of living systems that do not depend on sunlight. These are the denizens of chemosynthetic ecosystems hosted in the Earth’s dark, anoxic hydrothermal circulation zones. The discovery of a parallel chemosynthetic biosphere – around the same time as Carl Woese’s discovery of Archaea as the third domain of life, the invention of molecular phylogeny, and the discovery of ancient but previously unsuspected carbon fixation pathways including the reductive citric acid cycle –fundamentally reorganized our understanding of metabolic architecture to one centered in microbiology. From this perspective, core metabolism is a natural outgrowth of carbon fixation, and direct connections between geochemical redox reactions and biosynthesis are reconstructed at the base of all major lineages of life.
The discovery of ecosystems on Earth that do not depend on photosynthetically fixed carbon
Prior to the late 1970s, it was a pillar of biological thought that all life on Earth depended ultimately on the fixation of carbon into organic molecules by phototrophic organisms. Organisms that are not themselves photosynthesizers were believed to depend on organic carbon fixed by photosynthetic species, often incorporated with the aid of energy either from fermentation or respiration of organic carbon. The required oxidants were also due directly or indirectly to the activity of photosynthesizers. It thus came as shock when John Corliss and collaborators published a report in 1979 of a deep-sea submersible discovery of lush ecosystems surrounding hydrothermal vents at mid-ocean ridges. The primary producers are archaea and bacteria, nourished by volatiles released through magma degassing and dissolved nutrients from water/rock interactions that alter crust or mantle minerals. The whole-Earth redox disequilibrium, which is focused in the chemistry of vent environments delivers chemical energy sources to these organisms which constitute points of direct continuation from geochemistry to electron-transfer reactions in metabolism.
As of 2013, more than 150 active hydrothermal systems are known, in diverse tectonic settings, along the 60,000 km of ocean ridges and back-arc basins . Ecosystems at these sites are colonized not only by rich prokaryotic colonies, but in most cases also by a variety of annelid worms, mollusks, crustaceans, and other multicellular animals (some of them quite large), which may feed from microbial mats or host symbiotic microbes. As the microbiology and ecology of vent environments has become better understood in the ensuing three decades, some of the more productive vent communities have been discovered to have among the highest rates of carbon fixation known on earth, even though their contribution to total biotic carbon is small (∼0.02%) because of their restricted environments. This is an important observation though it has taken several years to become fully understood: it is not incidental that vent environments support extreme rates of primary productivity; they do so because in key respects biosynthesis is easier under the conditions created by hydrothermal circulation.
It is presumed that the early Earth would have had an atmosphere of simple gases of the type seen in space, or other planetary atmospheres, and/or predicted to be present based on models of how the Earth formed. Then, with these simple gases, you see if you can make biotic or prebiotic monomers by adding energy. Miller's spark discharge experiments (Miller 1953) were probably the first and certainly the most famous modern experimental attempt of that kind to make the primordial soup about which Darwin, Oparin and Haldane had written. The landmark Miller–Urey experiments showed how those first components of the first self-replicating molecule could easily be made by cooking up a little early Earth in a flask. The experiment consisted of running sparks (lightning) into a glass sphere (see figure 1) containing a reduced1 gas mixture of simple molecules, such as hydrogen, ammonia and methane (the atmosphere), connected by a tube to a reservoir of warm liquid water (the ocean). The results were breathtaking. When Miller analysed the organic matter that was made in that and subsequent experiments, he found certain amino acids, just the kind of thing that would have delighted Darwin. Starting with some simple common gases, a fairly minimal apparatus and a little energy, the fundamental components of proteins had formed rapidly. Although he was among the first to tackle the problem experimentally, and had only just begun, Miller had already made tremendous progress. Given that it was also the year that the structure of DNA was published, I am told that it seemed as if the secrets of life were being revealed and that very soon scientists would understand how life had come about. It turns out, of course, that the situation is not as straightforward as it may have appeared at that time. For one reason, the assumption that a mixture of reduced gases accurately represents the atmosphere of the early Earth has since been called into question.
Geologic data suggested that the Earth has been at or near its current oxidation state for over 3 and probably close to 4 billion years (Delano 2001), implying an atmosphere composed of neutral or perhaps even oxidized gases, such as H2O, CO2 and SO2. Such an oxidizing mixture on the early Earth would make it more difficult to make organic compounds like amino acids, by spark discharge. While most agree that the atmosphere was not reducing, on the other hand, there is no consensus that it was oxidizing either. Last year, there was a report asserting that even if the early atmosphere were dominated by CO2, the rate of escape of hydrogen from the Earth had been overestimated; therefore, more molecular hydrogen would have accumulated in the Earth's atmosphere than was previously thought. This hydrogen in turn would have allowed for some terrestrial synthesis of organic compounds (as simulated by spark discharge) albeit less efficiently than with the original Miller gas mixture.
Hydrothermal vents
In any case, if the spark discharge method of making organic molecules is not as important as it was originally thought to be, there are many other ways in which organic molecules may have formed on the early Earth. One very logical approach is to follow the hydrogen. Perhaps the most popular sites for potential organic synthesis in this vein are hydrothermal vents, and with good reason. Reducing gases emerge there, at least today, and presumably the early Earth was even more tectonically active than today, so, there would have been a great many of them early on.
The origin of life requires the formation of carbon-carbon bonds under primordial conditions 2 Miller’s experiments, in which simulating electric discharges in a reducing atmosphere of CH4, NH3, and H2O produced an aqueous solution of simple carboxylic acids and amino acids, have long been considered as one of the main pillars of the theory of a heterotrophic origin of life in a prebiotic broth. Their prebiotic significance, however, is in question, because it is now thought that the primordial atmosphere consisted mostly of an unproductive mixture of CO2, N2, and H2O, with only traces of molecular hydrogen. An alternative theory is that life had a chemoautotrophic origin.
The fixation of Co2 into living matter sustains all life on Earth, and embeds the biosphere within geochemistry. 1 The six known chemical pathways used by extant organisms for this function are recognized to have overlaps, but their evolution is incompletely understood. Here we reconstruct the complete early evolutionary history of biological carbon-fixation, relating all modern pathways to a single ancestral form. We find that innovations in carbon-fixation were the foundation for most major early divergences in the tree of life. These findings are based on a novel method that fully integrates metabolic and phylogenetic constraints. Comparing gene-profiles across the metabolic cores of deep-branching organisms and requiring that they are capable of synthesizing all their biomass components leads to the surprising conclusion that the most common form for deep-branching autotrophic carbon-fixation combines two disconnected sub-networks, each supplying carbon to distinct biomass components. One of these is a linear folate-based pathway of An external file that holds a picture, illustration, etc. Co2 reduction previously only recognized as a fixation route in the complete Wood-Ljungdahl pathway, but which more generally may exclude the final step of synthesizing acetyl-CoA. Using metabolic constraints we then reconstruct a “phylometabolic” tree with a high degree of parsimony that traces the evolution of complete carbon-fixation pathways, and has a clear structure down to the root. This tree requires few instances of lateral gene transfer or convergence, and instead suggests a simple evolutionary dynamic in which all divergences have primary environmental causes. Energy optimization and oxygen toxicity are the two strongest forces of selection. The root of this tree combines the reductive citric acid cycle and the Wood-Ljungdahl pathway into a single connected network. This linked network lacks the selective optimization of modern fixation pathways but its redundancy leads to a more robust topology, making it more plausible than any modern pathway as a primitive universal ancestral form.
The universal character of metabolism is, on the one hand, both a stronger and more striking fact of life from the vantage point of modern molecular biology than Donald Nicholson could have foreseen when he began his compilations more than a half-century ago, and on the other hand, it is a challenging regularity to express precisely. Many metabolites required by all organisms, if traced to their ultimate origin in CO2 and other inorganic inputs, require some key intermediates or reaction sequences that show no variation among known organisms. In autotrophic organisms they may be synthesized directly along these essential pathways, while in heterotrophs the dependence may be very indirect, involving multiple species and trophic exchanges, salvage pathways, and other such twists and turns, making general statements difficult in biology. Universal constraints on synthesis exist, but they require the correct unit of analysis and aggregation scale to express in rules. For this purpose, biological units such as organisms are not always the appropriate ones. For some essential functions such as carbon fixation, it would be incorrect to say that any single pathway, defined as a sufficiently complete reaction sequence to provide this function, is required by all living systems, even indirectly. Six pathways are now known to support autotrophic carbon fixation, which are in part genuinely different and independent. Yet the variations are mostly minor; all carbon fixation pathways show large overlaps of reaction sequences, and even larger homologies of reaction mechanisms and local-group chemistry. Where truly significant innovations have occurred, they appear to have been constrained to integrate within the same overall system, and therefore they feed their products back through a small standard set of precursors to anabolism and other key intermediates. For such cases, universality is not a property of any particular pathway, but must be recognized in the relations among pathways and the rules that have apparently governed the evolution of variants.
THE CARBON CYCLE 20
As already suggested, this means more than just headaches and high insurance fees for people living close to major fault lines. Plate tectonics makes possible the carbon cycle, which is essential to our planet’s habitability. This cycle is actually composed of a number of organic and inorganic subcycles, all occurring on different time scales. These cycles regulate the exchange of carbon-containing molecules among the atmosphere, ocean, and land. Photosynthesis, both by land plants and by phytoplankton near the ocean surface, is especially important since its net effects are to draw carbon dioxide from the atmosphere and make organic matter. Zooplankton, such as the forms mentioned in Chapter Two, consume much of the organic matter produced in the sunlight-rich surface. The carbonate and silicate skeletons of the marine organisms settle obligingly on the ocean floor, to be eventually squirreled away beneath the continents. Also central to the carbon cycle is the chemical weathering of silicate rocks on the continents.21 This occurs when rainwater, made acidic with dissolved carbon dioxide from the atmosphere, dissolves minerals in exposed rock. The rivers eventually carry dissolved silica (SiO2), calcium, and bicarbonate ions (derived from the carbon dioxide) to the oceans. Phytoplankton and zooplankton—and to a lesser extent, corals and shellfish— then remove these dissolved chemicals from the ocean to build their silicate and calcium carbonate skeletons. The carbon cycle is completed when the subducted carbonates are pressure-cooked deep in the crust, releasing carbon dioxide that eventually finds its way to the surface through volcanoes and springs. Negative feedback loops maintain the whole cycle in balance. Perhaps the most important stabilizing feedback is the dependence of the rate of chemical weathering on temperature. Here’s how it works: Suppose a prolonged period of large volcanic eruptions rapidly increased the amount of carbon dioxide in the atmosphere. Through the greenhouse effect, the upsurge in carbon dioxide would raise the global temperature. The higher temperature and carbon dioxide level, in turn, would speed up chemical weathering, and thus the removal of carbon dioxide from the atmosphere. Eventually, the carbon dioxide and temperature would return to their pre-eruption levels. Conversely, a drop in carbon dioxide would slow chemical weathering, allowing carbon dioxide to build up in the atmosphere. In either case, the loop comes full circle. As we’ll discuss in Chapter Four, a rise in atmospheric carbon dioxide increases plant growth. Rocks fuzzy with plants weather chemically about five times faster than bare rocks, allowing Earth to tuck carbon away under its surface all the more quickly. In other words, this accelerated weathering reinforces this stabilizing feedback loop, allowing Earth’s climate system to respond much more effectively to perturbations than could a lifeless world. Thus, plate tectonics, together with plant life, makes a planet much more nurturing for all life.
Sometimes, like in the Himalayas, continental plates thrust themselves into each other, and with nowhere to go but up, they build mountains. This is all essential for life on Earth. These processes carry carbon in and out of Earth's interior, and by doing so, regulate the amount of carbon dioxide in the atmosphere. Carbon dioxide is a greenhouse gas: too much of it, and the atmosphere traps too much heat. "The surface temperature increases and Earth eventually becomes a planet like Venus," says Jun Korenaga, a geophysicist at Yale University, US. Too little, and all the heat would escape, leaving Earth inhospitably cold. The carbon cycle therefore acts as a global thermostat, regulating itself when needed. A warmer climate also results in more rain, which helps extract more carbon dioxide out of the atmosphere.
The gas is dissolved in raindrops, which fall on exposed rock. Chemical reactions between the rainwater and rock release the carbon and minerals like calcium from the rock. The water then flows through rivers and streams, eventually reaching the ocean, where the carbon forms carbonate rocks and organic objects like seashells. The carbonate settles on the bottom of the ocean, on a tectonic plate that gets subducted, carrying the carbon into Earth's interior. Volcanoes then belch the carbon back into the atmosphere as carbon dioxide. Plate tectonics plays a part in every aspect of this cycle. Not only does subduction deliver carbon back into Earth's mantle, but tectonic activity brings fresh rock to the surface. That exposed rock is crucial for the chemical reactions that release minerals. Mountains, formed from plate tectonics, channel air upward, where it cools, condenses, and forms raindrops – which help extract carbon from the atmosphere. 21
1. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3334880/
2. http://fire.biol.wwu.edu/cmoyer/zztemp_fire/biol345_S99/huber1.pdf
3. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC1664678/
4. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC1664679/
5. https://en.wikipedia.org/wiki/Carbon_cycle
6. http://www.ams.org/journals/bull/2015-52-01/S0273-0979-2014-01471-5/S0273-0979-2014-01471-5.pdf
7. http://www.informationphilosopher.com/solutions/scientists/hartman/Metabolism.pdf
8. http://jcourtneywhite.com/wp-content/uploads/2016/09/The_Story_of_Carbon.pdf
9. https://www.sciencedaily.com/releases/2014/03/140319143904.htm
10. A privildedged plantet, Gonzalez, page 55
11. http://www.nationalgeographic.org/media/plankton-revealed/
12. http://www.mintpressnews.com/the-fabulous-history-of-plankton-and-why-our-survival-depends-on-it/44732/
13. https://www.guam.net/pub/sshs/depart/science/mancuso/apbiolecture/03_carbon/carbon.htm
14. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4283042/
15. Environmental microbiology, page 38
16. http://www.nature.com/nature/journal/v459/n7244/full/nature08057.html
17. http://creation.com/gods-micro-world
18. http://www2.cnrs.fr/en/519.htm
19. http://www.livescience.com/46250-teasing-apart-the-diatom-genome.html
20. Privileged Planet, Gonzalez, page 55
21. http://www.bbc.com/earth/story/20170111-the-unexpected-ingredient-necessary-for-life
http://reasonandscience.heavenforum.org/t2464-the-finely-tuned-carbon-cycle-essential-for-life
Carbon is present in all known life forms. It can be found dissolved in all water bodies on the planet. It is abundant in the Sun, stars, comets, meteorites, and in the atmospheres of most planets. Earth was just geology and chemistry – no biology. Then something happened to spark life, something mysterious. Between the geochemical origins of Earth and its eventual biological life is something scientists call a ‘black box’ – a figurative box they cannot peer into. Below the box are chemicals, above it DNA. The link is carbon, scientists agree, but how it happened precisely remains a mystery. The carbon in the atmosphere, the oceans, the trees, the soils, us and everything else is constantly in motion, flowing in a giant circle from air to land and back to air again in an unending, closed loop. The Law of the Conservation of Matter says that in a closed system matter can neither be created or destroyed. It can only cycle and recycle. The Earth has been a closed system almost from its origin with only solar energy, an occasional electromagnetic pulse from the sun, and stray bits of asteroids and comets entering from space. What’s here now has always been here, including carbon whose total amount is essentially the same as it was when Earth formed 4.5 billion years ago.
And what carbon does is cycle, a process essential to life on Earth. It’s a carefully regulated process so that the planet can maintain critical balances. Call it the Goldilocks Principle: not too much carbon, not too little, but just the right amount. For instance, without CO2 and other greenhouse gases Earth would be a frozen ball of rock. With too many greenhouse gases, however, Earth would be like hothouse Venus. Just right means balancing between the two extremes, which helps to keep the planet’s temperature relatively stable. It’s like the thermostat in your house. If it gets too warm, the cycle works to cool things off and vice versa. Of course, the planet’s thermostat gets overwhelmed at times, resulting periods of rapid warming or cooling (think Ice Ages).
Carbon Compounds in Cells 13
Carbon has unique quantum properties that make it the backbone of all organic compounds. It cycles through the atmosphere and the biomass of living organisms through various biochemical pathways. Its used for simple sugars like monosaccharides ( Ribose deoxyribose (five-carbon backbones) - building blocks for nucleic acids ) , Short-Chain Carbohydrates ( oligosaccharides, like lactose, sucrose, maltose ) Complex Carbohydrates ( polysaccharides like starch, cellulose, glycogen, chitin ), Lipids like fatty acids, Triglycerides (Neutral Fats), Phospholipids, Sterols and Their Derivatives, Waxes, proteins, nucleotides and amino acids.
Goldilocks principle: Earth's continued habitability due to geologic cycles that act as climate control 9
Scientists have shown how geologic process regulates the amount of carbon dioxide in the atmosphere. Researchers have documented evidence suggesting that part of the reason that Earth has become neither sweltering like Venus nor frigid like Mars lies with a built-in atmospheric carbon dioxide regulator — the geologic cycles that churn up the planet’s rocky surface.
The men who first proposed in some detail the heterotrophic origin of life were Haldane (1928) and Oparin (1924). Haldane (1928) proposed that, in the absence of oxygen, U.V. acting on a mixture of carbon dioxide, ammonia, and water would yield a large variety of organic compounds, including amino acids and sugars. These compounds would have accumulated in the oceans until they reached the consistency of hot dilute soup. The first organisms were large molecules synthesized under the influence of sunlight and were capable of replication in this rich medium. By mutation and selection the first cell arose and then gradually evolved a photosynthetic capacity as the rich medium became used up. Photosynthesis led to the production of oxygen and thus accounted for the present level of oxygen in our atmosphere. This picture is the dominant view held today. The only modification was made by the experiments of Miller (1955), where the atmosphere was methane, ammonia, and hydrogen. The main problem which is left is the appearance of a molecule which is capable of self-reproduction. The best guess is that it was an RNA molecule (Crick, 1968; Orgel, 1968). This RNA molecule would then evolve by mutation and selection until it coupled with proteins by means of a primitive genetic code. The evolution of metabolism, anabolic and catabolic, is one of a gradual development of autotrophy from the initial heterotrophy, again by a process of mutation and selection as the soup became depleted (Horowitz, 1945).
Plate tectonics makes possible the carbon cycle, which is essential to our planet’s habitability. 10 This cycle is actually composed of a number of organic and inorganic subcycles, all occurring on different timescales. These cycles regulate the exchange of carbon-containing molecules among the atmosphere, ocean, and land. Photosynthesis, both by land plants and by phytoplankton near the ocean surface, is especially important, since its net effects are to draw carbon dioxide from the atmosphere and make organic matter. Zooplankton consume much of the organic matter produced in the sunlight-rich surface. The carbonate and silicate skeletons of the marine organisms settle obligingly on the ocean floor, to be eventually squirreled away beneath the continents.
MICROBIAL DECOMPOSERS: FUNDAMENTAL for the Earth's biogeochemical cycles 14
All living organisms depend on the supply of necessary elements from the Earth. Since the Earth is a closed system with a finite supply of essential elements such as hydrogen (H), oxygen (O), carbon (C), nitrogen (N), sulfur (S) and phosphorus (P), recycling of these elements is fundamental to avoid exhaustion.
Beside the Nitrogen cycle, silicon cycle, water cycle, Phosphorus, Iron, and Trace Mineral cycles , the global carbon cycle is essential for life on earth. How was it all setup ? Design, or a giant lucky accident ?!
Carbon is the fourth most abundant element in the universe, the fifteenth most abundant element on Earth, and the second most abundant in the human body after oxygen. 8 Carbon is present in all known life forms. It can be found dissolved in all water bodies on the planet. It is abundant in the Sun, stars, comets, meteorites, and in the atmospheres of most planets. Carbon is star dust. It first formed in the interiors of stars not long after the Big Bang and then scattered into space as dust as a result of supernova explosions. Over time, it coalesced into star systems such as ours, as well as planets, comets, and other heavenly bodies. Eventually, it coalesced into us. Carbon is life. It exists in every organic life form. Life is impossible without it.
Carbon Compounds in Cells 13
Carbon has unique quantum properties that make it the backbone of all organic compounds. It cycles through the atmosphere and the biomass of living organisms through various biochemical pathways. Its used for simple sugars like monosaccharides ( Ribose deoxyribose (five-carbon backbones) - building blocks for nucleic acids ) , Short-Chain Carbohydrates ( oligosaccharides, like lactose, sucrose, maltose ) Complex Carbohydrates ( polysaccharides like starch, cellulose, glycogen, chitin ), Lipids like fatty acids, Triglycerides (Neutral Fats), Phospholipids, Sterols and Their Derivatives, Waxes, proteins, nucleotides and amino acids.
When combined with water it forms sugars, fats, alcohols, fats, and terpenes. When combined with nitrogen and sulfur it forms amino acids, antibiotics, and alkaloids. With the addition of phosphorus, it forms DNA and RNA – the essential codes of life – as well as ATP, the critical energy-transfer molecule found in all living cells. The carbon atom is the essential building block of life. Every part of your body is made up of chains of carbon atoms, which is why we are known as “carbon-based life forms.” We are star dust.
Carbon is a miracle. Chemically, we’re just a bunch of inert compounds. What breathes life into us? The answer is the relationship between the molecules of energy and nutrients fueled by carbon and water. Billions of years ago, Earth was just geology and chemistry – no biology. Then something happened to spark life, something mysterious. Between the geochemical origins of Earth and its eventual biological life is something scientists call a ‘black box’ – a figurative box they cannot peer into. Below the box are chemicals, above it DNA. The link is carbon, scientists agree, but how it happened precisely remains a mystery. The carbon in the atmosphere, the oceans, the trees, the soils, us and everything else is constantly in motion, flowing in a giant circle from air to land and back to air again in an unending, closed loop. The Law of the Conservation of Matter says that in a closed system matter can neither be created or destroyed. It can only cycle and recycle. The Earth has been a closed system almost from its origin with only solar energy, an occasional electromagnetic pulse from the sun, and stray bits of asteroids and comets entering from space. What’s here now has always been here, including carbon whose total amount is essentially the same as it was when Earth formed 4.5 billion years ago.
And what carbon does is cycle, a process essential to life on Earth. It’s a carefully regulated process so that the planet can maintain critical balances. Call it the Goldilocks Principle: not too much carbon, not too little, but just the right amount. For instance, without CO2 and other greenhouse gases Earth would be a frozen ball of rock. With too many greenhouse gases, however, Earth would be like hothouse Venus. Just right means balancing between the two extremes, which helps to keep the planet’s temperature relatively stable. It’s like the thermostat in your house. If it gets too warm, the cycle works to cool things off and vice versa. Of course, the planet’s thermostat gets overwhelmed at times, resulting periods of rapid warming or cooling (think Ice Ages).
Goldilocks principle: Earth's continued habitability due to geologic cycles that act as climate control 9
Scientists have shown how geologic process regulates the amount of carbon dioxide in the atmosphere. Researchers have documented evidence suggesting that part of the reason that Earth has become neither sweltering like Venus nor frigid like Mars lies with a built-in atmospheric carbon dioxide regulator — the geologic cycles that churn up the planet’s rocky surface.
Scientists have long known that “fresh” rock pushed to the surface via mountain formation effectively acts as a kind of sponge, soaking up the greenhouse gas CO2. Left unchecked, however, that process would simply deplete atmospheric CO2 levels to a point that would plunge Earth into an eternal winter within a few million years during the formation of large mountain ranges like the Himalayas — which has clearly not happened.
And while volcanoes have long been pointed to as a source of carbon dioxide, alone they cannot balance out the excess uptake of carbon dioxide by large mountain ranges. Instead, it turns out that “fresh” rock exposed by uplift also emits carbon through a chemical weathering process, which replenishes the atmospheric carbon dioxide at a comparable rate.
Fortunately, the miraculous carbon cycles keeps working, scrubbing excess CO2 out of the atmosphere or adding more if necessary. Who does all this regulatory work? green, growing plants and. Photosynthesis is the process by which carbon is transferred from sky to soil. It’s what makes the Goldilocks principle tick. It keeps the Goldilocks principle ticking over time – long periods of time. The two work in concert. The greenhouse effects of an excessive build up of CO2 in the atmosphere, for instance, will impact the fate of generations of living things. Carbon and life interact and adjust to each other, regulating and responding in a sophisticated dance. Carbon chooses the music, if you will, while evolution dictates the steps in a planetwide choreography. It is a dance with a profound effect on audience members.
Carbon is not the only dance on the planet, of course. Our world is full of cycles – water, energy, nutrients, nitrogen, phosphorus, and many more – interacting with each other in complicated ways. Carbon has both. Its short, or fast, cycle revolves around green plants and photosynthesis – the process by which carbon is separated from oxygen, stored in roots and soils, and released back into the atmosphere via death and decomposition.
The process by which atmospheric CO2 gets converted into soil carbon requires is sunlight, green plants, water, nutrients, and soil microbes. There are four basic steps to the CO2 / soil carbon cycle:
Photosynthesis: This is the process by which energy in sunlight is transformed into biochemical energy in the form of a simple sugar called glucose via green plants – which use CO2 from the air and water from the soil, releasing oxygen as a by-product. The chemical reaction looks like this: CO2 + H2O + energy = CH2O + O2
Resynthesis: Through a complex sequence of chemical reactions, glucose is resynthesized into a wide variety of carbon compounds, including carbohydrates (such as cellulose and starch), proteins, organic acids, waxes, and oils (including hydrocarbons), all of which serve as ‘fuel’ for life on Earth.
Exudation: Carbon created by photosynthesis can be exuded directly into soil by plant roots to nurture microbes and other organisms. This process is essential to the creation of soil from the lifeless mineral soil produced by the weathering of rocks over time. The amount of increase in organic carbon is governed by the volume of plant roots per unit of soil and their rate of growth. More active green leaves mean more roots, which mean more carbon exuded.
Humification: or the creation of humus – a chemically stable type of organic matter composed of large, complex molecules made up of carbon, nitrogen, minerals, and soil particles. Visually, humus is the dark, rich layer of topsoil that people generally associate with stable wetlands, healthy rangelands, and productive farmland. Once carbon is stored as humus it has a high resistance to decomposition, and therefore can remain intact and stable for hundreds or thousands of years.
Let’s follow three carbon molecules from the air to three separate destinations. Imagine these molecules enjoying a carefree life as a gas, each accompanied by two oxygen molecules, as they joyride side-by-side through the air without a care in the world. Suddenly, all three smack into a green, leafy something and quickly pass from the bright light of the atmosphere into the dark, vascular world of a plant. Now their carefree existence turns into a wild toboggan ride of photosynthesis. The three molecules go through a series of transformative twists, turns, and drops as they travel through the plant, bathed in green, drenched in water, stripped of their oxygen buddies, and eventually picking up new molecular passengers, including hydrogen, nitrogen, and more carbon. At the end of their wild ride, the molecules are no longer part of a gas having become instead part of a sugary carbohydrate called glucose, a vital source of energy for the plant. At this point a new ride begins and our three carbon molecules are quickly sent in three separate directions. The first molecule concludes its journey in a leaf cell, where the glucose is converted by the plant into a kind of biological battery called starch which it stores for later use, such as winter when photosynthesis is turned off. Other uses of glucose by the plant include respiration, creating the sweetness in fruit, conversion into cellulose for cell-wall strengthening, forming fatty lipids for storage in seeds, and generating proteins, which are an important source of food for all living things. In this case, our carbon molecule rests quietly in its cell waiting to be summoned when the leaf is suddenly ripped from its host by a hungry herbivore. After a brief but tumultuous ride through grinding teeth, the molecule slides downward into a smelly stomach and eventually passes into the animal’s digestive tract, where the starch is processed and the carbon absorbed into a cell of muscle tissue. A month later, the cycle is completed when the animal breaks a leg and dies in the wild. As it decomposes, the carbon molecule is exposed to the air where it picks up two oxygen atoms swinging by and together they rise upward to begin the joyride all over again.
The second carbon molecule shoots underground through the plant’s stem and then slows to a crawl as it reaches the tip of a slender root. The plant intends to use the glucose to build new root mass so it can tap additional water and nutrients, but before it can the plant suddenly shudders as half of its leaves are wrenched away by the hungry herbivore. This causes the plant to send an emergency signal to its roots: retreat! To help recover its vigor and grow new leaves again, the plant must now use the glucose stored in its root cellar, ordering the supplies upward. It’s not a crisis however (unless the hungry herbivore comes back around for a second bite) because by removing last year’s dead material along with this year’s green growth, the herbivore has freed up the plant to grow unimpeded. One of the plant’s first responses is to slough off the tips of its roots to conserve energy. That means our second carbon molecule finds itself detached and isolated from the rest of the plant, lost and lonely in the soil – but not for long. Soon, the decaying root tips attract the attention of a host of hungry microbes and other critters, including protozoa, nematodes, fungi, earthworms, arthropods, and a huge variety of bacteria (there are more microbes in a teaspoon of soil than humans on the planet). Bacteria go to work first. These are single-celled creatures with one goal in mind: eat! They are particularly ravenous for carbon and after they have digested a bunch of it they become attractive to predatory critters in the neighborhood. Soon, a feeding frenzy begins. Our particular carbon molecule disappears down the throat of a nematode, which is a type of tiny worm. There are approximately one million different species of nematodes on the planet, found in every type of ecosystem, accounting for 80 percent of all creatures in existence on Earth. That makes for a lot of eating and pooping going on below ground.
In this case, the nematode eventually excretes our molecule into the soil where it bonds with two sly oxygen molecules hanging out (smoking cigarettes) in the tiny air pockets between soil particles and becomes part of a carbon dioxide molecule once again. Eventually this new CO2 molecule makes its way up to the soil surface and back into the atmosphere – a process scientists call soil respiration – to join zillions of their buddies for another wild ride. Round and round. Meanwhile, our third carbon molecule has followed a similar path to the plant’s roots, only to end up inside a fungus instead of a nematode – and not just any fungus, but one of the heroic mycorrhizal varieties. These are long, skinny filaments that live on the surface of plant 17 roots with which they share a symbiotic relationship, trading essential nutrients and minerals back and forth (mycorrhiza is Greek for fungus + root, or “I’ll scratch your carbon if you’ll scratch mine”). The fungus-root mutualism reduces a plant’s susceptibility to disease while and increasing its tolerance to adverse conditions, including prolonged drought spells or salty soils. Fungi in general are best known to humans as the source of mushrooms, yeasts, and the molds that make cheeses tasty, ruin houses in humid climates, and produce antibiotics. Like plants and animals, fungi form their own taxonomic kingdom. In fact, there are an estimated two to five million individual species of fungi on the planet, of which less than 5% have been formally classified by taxonomists. In the soil, fungi can be “good guys” or “bad guys” depending on your perspective (the “bad guys” cause a variety of diseases). Our third carbon molecule ends up in a good guy called an arbuscular mycorrhizal fungus. After absorbing the bit of glucose containing our molecule from the plant root, the skinny arbuscular fungus next pushes the carbon into one of its hyphae – hair-like projections that extend as much as two inches into the soil in a never-ending search for nutrients. Then, in a process that is not completely understood by scientists the carbon molecule is extruded into the soil from the hyphae in a sticky protein called glomalin – one of nature’s superglues. You can feel glomalin. It’s what gives soil its tilth – the rich, smooth texture that tells experienced farmers and gardeners that they holding great soil in their hands. To create tilth, the soil engine needs both biology and chemistry working together and glomalin is the glue that binds them. It’s an extraordinary process, one which creates a world of possibilities!
Identification of how and where carbon occurs within an environment is an important signal to know whether the setting is, or is capable of, hosting life. On Earth today, there are three major carbon-bearing reservoirs that are interrelated: the atmosphere; the hydrosphere; and the litosphere. Superimposed on these, and acting throughout, is the biosphere. 4 We now know that comet and asteroid dust deliver tons of organics to the Earth every day, therefore this flux of reduced carbon from space probably also played a role in making the Earth habitable. 3
In the speculations on the origin of life, the most difficult conceptual problems deal with the complexity of the first organism and the complexity of its environment. 7 There are four possibilities:
(I) the first organism was simple (e.g., RNA) and its environment was complex (heterotrophic origin);
(2) the organism was simple (e.g., clays) and its environment was simple (autotrophic origin);
(3) the organism was complex and its environment was complex (heterotrophic panspermia);
(4) the organism was complex and its environment was simple (autotrophic panspermia).
The men who first proposed in some detail the heterotrophic origin of life were Haldane (1928) and Oparin (1924). Haldane (1928) proposed that, in the absence of oxygen, U.V. acting on a mixture of carbon dioxide, ammonia, and water would yield a large variety of organic compounds, including amino acids and sugars. These compounds would have accumulated in the oceans until they reached the consistency of hot dilute soup. The first organisms were large molecules synthesized under the influence of sunlight and were capable of replication in this rich medium. By mutation and selection the first cell arose and then gradually evolved a photosynthetic capacity as the rich medium became used up. Photosynthesis led to the production of oxygen and thus accounted for the present level of oxygen in our atmosphere. This picture is the dominant view held today. The only modification was made by the experiments of Miller (1955), where the atmosphere was methane, ammonia, and hydrogen. The main problem which is left is the appearance of a molecule which is capable of self-reproduction. The best guess is that it was an RNA molecule (Crick, 1968; Orgel, 1968). This RNA molecule would then evolve by mutation and selection until it coupled with proteins by means of a primitive genetic code. The evolution of metabolism, anabolic and catabolic, is one of a gradual development of autotrophy from the initial heterotrophy, again by a process of mutation and selection as the soup became depleted (Horowitz, 1945).
The Carbon cycle 5
The carbon cycle is the biogeochemical cycle by which carbon is exchanged among the biosphere, pedosphere, geosphere, hydrosphere, and atmosphere of the Earth. Along with the nitrogen cycle and the water cycle, the carbon cycle comprises a sequence of events that are key to make the Earth capable of sustaining life; it describes the movement of carbon as it is recycled and reused throughout the biosphere, including carbon sinks.
Under terrestrial conditions, conversion of one element to another is very rare. Therefore, the amount of carbon on Earth is effectively constant. Thus, processes that use carbon must obtain it from somewhere and dispose of it somewhere else. The paths of carbon in the environment form the carbon cycle. For example, photosynthetic plants draw carbon dioxide from the atmosphere (or seawater) and build it into biomass, as in the Calvin cycle, a process of carbon fixation. Some of this biomass is eaten by animals, while some carbon is exhaled by animals as carbon dioxide. The carbon cycle is considerably more complicated than this short loop; for example, some carbon dioxide is dissolved in the oceans; if bacteria do not consume it, dead plant or animal matter may become petroleum or coal, which releases carbon when burned
Plants, fueled by the Sun’s radiation, convert CO2 to sugar and other carbohydrates by photosynthesis. 6 Organisms that consume plants derive their energy from the oxidation of those photosynthetic products. Further up the food chain, organisms that consume other consumers ultimately derive their energy from the same source. In these ways, the CO2 that had been taken out of the atmosphere and oceans by plants is returned from where it came; the process is called respiration. Integrated over all organisms and all environments, the loop between photosynthesis and respiration makes up the biological component of Earth’s carbon cycle.
Carbon-bearing reservoirs on Earth
Schematic representation of the pathways through which the carbon cycles operate on Earth today.
Evidence for the earliest existence of water comes from the oxygen isotopic composition of the mineral zircon present in meta-sediments from the Jack Hills Formation of Western Australia. Most of these grains are around 4.2 Gyr old, but there are some detrital zircons with ages as ancient as 4.4 Gyr and their presence implies the existence of a fairly widespread ocean, as well as reworked crustal sediments . Therefore, by 4.4 Gyr ago, Earth already had an atmosphere, a lithosphere and a hydrosphere, and the reservoirs were actively connected. Tectonic activity occurred, where crust was subducted and recycled, but plate tectonics was not completely established. At some point between the formation and 3.5 Gyr ago, Earth had stabilized to the extent that there were three dynamically interacting reservoirs: the atmosphere, the lithosphere and the hydrosphere; and plate tectonics was taking place with a mechanism of plate movement close to that which is in operation today.
The mechanism of photosynthesis acts to remove CO2 from the atmosphere and replenishes it with oxygen. This reaction is balanced by respiration, which removes O2 from the atmosphere and replaces with CO2. As the biomass of photosynthesizing organisms increased, there was an increasing ‘fixing’ of carbon by burial, as the micro-organisms lived and died, gradually increasing the oxygen content of Earth's atmosphere. At around 2.3 Gyr ago, the switch from a reducing to an oxidizing atmosphere became permanent, and the atmosphere had evolved to a composition closer to that observed today (Holland 2002). The unambiguous establishment of life can be tracked through the fossil record, with the first appearance of macro-fossils ca 600 Myr ago (e.g. Conway Morris 1993). Through time, variations in global climate, impacts and tectonic processes have changed the surface of the Earth, and species have evolved and become extinct. However, overall, since the biosphere became established and the atmosphere oxidizing, there have been no gross changes to the way in which the terrestrial carbon cycles have operated.
Plate tectonics makes possible the carbon cycle, which is essential to our planet’s habitability. 10 This cycle is actually composed of a number of organic and inorganic subcycles, all occurring on different timescales. These cycles regulate the exchange of carbon-containing molecules among the atmosphere, ocean, and land. Photosynthesis, both by land plants and by phytoplankton near the ocean surface, is especially important, since its net effects are to draw carbon dioxide from the atmosphere and make organic matter. Zooplankton consume much of the organic matter produced in the sunlight-rich surface. The carbonate and silicate skeletons of the marine organisms settle obligingly on the ocean floor, to be eventually squirreled away beneath the continents.
Plankton Revealed - A critical component of life on Earth 11
Plankton are an essential component of life on Earth. Marine plankton, found in all ocean ecosystems, play a critical role in maintaining the health and balance of the ocean and its complex food webs. The oxygen, nutrients, and biomass they produce also sustain terrestrial life—from the food we eat to the air we breathe. With 71% of the Earth covered by the ocean, phytoplankton are responsible for producing up to 50% of the oxygen we breathe. These microscopic organisms also cycle most of the Earth’s carbon dioxide between the ocean and atmosphere. Plankton also play a role at the end of the food web—as decomposers and detritivores. These plankton, including bacteria, fungi, and worms, break down and consume dead plant and animal material that falls through the water column as "marine snow." Marine snow often includes fecal matter, sand, soot, skin, and other organic and inorganic particles descending to the seafloor.
Without plankton, we as human beings would not be here; and without them, we’d probably disappear. So we’d better be aware of what happens to them, including what we do to them. 12 “These tiny living organisms, when they die, sediment at the bottom of the oceans. With time, the accumulated sediments generate different kinds of rocks like limestone, chalk and opal. We now find rock structures all over the world composed of billions of these microscopic organisms, such as the white cliffs of Dover in England, or the Sisquoc formation in Lompoc, Santa Barbara. Most of northern Europe is actually of planktonic origin.”
First, we have what we call the protists, mainly the phytoplankton, if you want. There are up to 10 million of them in every liter of seawater. Then we have the metazoans, like the zooplankton, which graze on the protists. We also have bacteria – up to 1 billion/liter – and viruses – up to 10 billion/liter. These viruses are not dangerous for human beings, only for the phytoplankton and the zooplankton. They have an important regulatory role because they maintain the turnover in the system. Nature does not tolerate excess, it likes equilibrium between species. This means that as soon as one species becomes dominant, nature finds a way to eliminate it.”
First, and this is probably the most obvious one, they are at the base of the food chain. They provide food to the fish which we eat. Second, they still generate half of the oxygen on the planet, removing CO2 from the atmosphere in the process. We know why this is so important: Carbon dioxide, being a greenhouse gas, is contributing to the global warming of the Earth. Hence the importance of reducing its presence in the atmosphere. “That forests are the first lung of our planet is well-known; what is much less known is that oceans constitute the second. It is like an invisible forest in the oceans,” says Bowler.
Also central to the carbon cycle is the chemical weathering of silicate rocks on the continents. This occurs when rainwater, made acidic with dissolved carbon dioxide from the atmosphere, dissolves minerals in exposed rock. The rivers eventually carry dissolved silica (SiO2), calcium, and bicarbonate ions (derived from the carbon dioxide) to the oceans. Phytoplankton and zooplankton—and to a lesser extent, corals and shellfish— then remove these dissolved chemicals from the ocean to build their silicate and calcium carbonate skeletons. The carbon cycle is completed when the subducted carbonates are pressure-cooked deep in the crust, releasing carbon dioxide that eventually finds its way to the surface through volcanoes and springs.
As an example, diatoms are the major phytoplankton group that play a role in maintaining oxygen levels in the atmosphere and in the carbon cycle that sustains primary production in aquatic environments. The most abundant diatom is Chaetocerus 15
Diatoms
Diatoms are one of the most important lifeforms on the planet. These single celled organisms have shells of silica and make almost half of all the organic compounds produced in the ocean. These are just a few of the reasons why plankton deserve the title “Earth’s most important creatures”. Plankton are responsible for 50% of earth’s oxygen. They are an essential part of the food chain. And billions of billions of ancient plankton have given their bodies to form the crude oil that powers modern society. Yet we rarely recognise their contribution to life on this planet, including our own.
No one really knows how many different diatoms are out there, but conservative estimates suggest around 100,000 to 200,000 species, making them among the most species-rich lineages of eukaryotes. 19
God’s micro world 17
Diatoms are marvels of complex architectural engineering. They have the unique ability to fashion intricate glass-houses for themselves by using the silica found naturally in sea-water. Not only are they intricately built, but they are found in all known geometrical shapes and are symmetrical in three dimensions, having perfectly matched tops and bottoms that are held together until the plant dies and the two halves come apart. Very rarely in biological systems do you find the use of straight lines for structural support. But diatoms are masters, not only at straight lines, but also at circles, triangles, squares, and ovals.
Diatoms have a sophisticated calcium and nitric oxide-based surveillance system for monitoring environmental stresses that can detect the release of aldehydes by its wounded neighbours. 18
The life of diatoms in the world’s oceans 16
More on How Microbes Make Earth Habitable
These Kaleidoscopic Masterpieces Are Invisible to the Naked Eye
The amazing diversity and beauty of Diatoms
MICROBIAL DECOMPOSERS: FUNDAMENTAL for the Earth's biogeochemical cycles 14
All living organisms depend on the supply of necessary elements from the Earth. Since the Earth is a closed system with a finite supply of essential elements such as hydrogen (H), oxygen (O), carbon (C), nitrogen (N), sulfur (S) and phosphorus (P), recycling of these elements is fundamental to avoid exhaustion. Microbes are critical in the process of breaking down and transforming dead organic material into forms that can be reused by other organisms. This is why the microbial enzyme systems involved are viewed as key ‘engines’ that drive the Earth's biogeochemical cycles.
The terrestrial carbon cycle is dominated by the balance between photosynthesis and respiration. Carbon is transferred from the atmosphere to soil via ‘carbon-fixing’ autotrophic organisms, mainly photosynthesising plants and also photo- and chemoautotrophic microbes,that synthesise atmospheric carbon dioxide (CO2) into organic material. Fixed carbon is then returned to the atmosphere by a variety of different pathways that account for the respiration of both autotrophic and heterotrophic organisms. The reverse route includes decomposition of organic material by ‘organic carbon-consuming’ heterotrophic microorganisms that utilise the carbon of either plant, animal or microbial origin as a substrate for metabolism, retaining some carbon in their biomass and releasing the rest as metabolites or as CO2 back to the atmosphere
Negative feedback loops maintain the whole cycle in balance. Perhaps the most important stabilizing feedback is the dependence of the rate of chemical weathering on temperature. Here’s how it works: Suppose a prolonged period of large volcanic eruptions rapidly increased the amount of carbon dioxide in the atmosphere. Through the greenhouse effect, the upsurge in carbon dioxide would raise the global temperature. The higher temperature and carbon dioxide level, in turn, would speed up chemical weathering, and thus the removal of carbon dioxide from the atmosphere. Eventually, the carbon dioxide and temperature would return to their preeruption levels. Conversely, a drop in carbon dioxide would slow chemical weathering, allowing carbon dioxide to build up in the atmosphere. In either case, the loop comes full circle. Thus, plate tectonics, together with plant life, makes a planet much more nurturing for all life.
The parallel biosphere of chemotrophy on Earth
Within only the past 30 years, an understanding of the biosphere has become possible that completely inverts the view that had been accreting for more than a century. A pivotal event in this reframing was the discovery of living systems that do not depend on sunlight. These are the denizens of chemosynthetic ecosystems hosted in the Earth’s dark, anoxic hydrothermal circulation zones. The discovery of a parallel chemosynthetic biosphere – around the same time as Carl Woese’s discovery of Archaea as the third domain of life, the invention of molecular phylogeny, and the discovery of ancient but previously unsuspected carbon fixation pathways including the reductive citric acid cycle –fundamentally reorganized our understanding of metabolic architecture to one centered in microbiology. From this perspective, core metabolism is a natural outgrowth of carbon fixation, and direct connections between geochemical redox reactions and biosynthesis are reconstructed at the base of all major lineages of life.
The discovery of ecosystems on Earth that do not depend on photosynthetically fixed carbon
Prior to the late 1970s, it was a pillar of biological thought that all life on Earth depended ultimately on the fixation of carbon into organic molecules by phototrophic organisms. Organisms that are not themselves photosynthesizers were believed to depend on organic carbon fixed by photosynthetic species, often incorporated with the aid of energy either from fermentation or respiration of organic carbon. The required oxidants were also due directly or indirectly to the activity of photosynthesizers. It thus came as shock when John Corliss and collaborators published a report in 1979 of a deep-sea submersible discovery of lush ecosystems surrounding hydrothermal vents at mid-ocean ridges. The primary producers are archaea and bacteria, nourished by volatiles released through magma degassing and dissolved nutrients from water/rock interactions that alter crust or mantle minerals. The whole-Earth redox disequilibrium, which is focused in the chemistry of vent environments delivers chemical energy sources to these organisms which constitute points of direct continuation from geochemistry to electron-transfer reactions in metabolism.
As of 2013, more than 150 active hydrothermal systems are known, in diverse tectonic settings, along the 60,000 km of ocean ridges and back-arc basins . Ecosystems at these sites are colonized not only by rich prokaryotic colonies, but in most cases also by a variety of annelid worms, mollusks, crustaceans, and other multicellular animals (some of them quite large), which may feed from microbial mats or host symbiotic microbes. As the microbiology and ecology of vent environments has become better understood in the ensuing three decades, some of the more productive vent communities have been discovered to have among the highest rates of carbon fixation known on earth, even though their contribution to total biotic carbon is small (∼0.02%) because of their restricted environments. This is an important observation though it has taken several years to become fully understood: it is not incidental that vent environments support extreme rates of primary productivity; they do so because in key respects biosynthesis is easier under the conditions created by hydrothermal circulation.
It is presumed that the early Earth would have had an atmosphere of simple gases of the type seen in space, or other planetary atmospheres, and/or predicted to be present based on models of how the Earth formed. Then, with these simple gases, you see if you can make biotic or prebiotic monomers by adding energy. Miller's spark discharge experiments (Miller 1953) were probably the first and certainly the most famous modern experimental attempt of that kind to make the primordial soup about which Darwin, Oparin and Haldane had written. The landmark Miller–Urey experiments showed how those first components of the first self-replicating molecule could easily be made by cooking up a little early Earth in a flask. The experiment consisted of running sparks (lightning) into a glass sphere (see figure 1) containing a reduced1 gas mixture of simple molecules, such as hydrogen, ammonia and methane (the atmosphere), connected by a tube to a reservoir of warm liquid water (the ocean). The results were breathtaking. When Miller analysed the organic matter that was made in that and subsequent experiments, he found certain amino acids, just the kind of thing that would have delighted Darwin. Starting with some simple common gases, a fairly minimal apparatus and a little energy, the fundamental components of proteins had formed rapidly. Although he was among the first to tackle the problem experimentally, and had only just begun, Miller had already made tremendous progress. Given that it was also the year that the structure of DNA was published, I am told that it seemed as if the secrets of life were being revealed and that very soon scientists would understand how life had come about. It turns out, of course, that the situation is not as straightforward as it may have appeared at that time. For one reason, the assumption that a mixture of reduced gases accurately represents the atmosphere of the early Earth has since been called into question.
Geologic data suggested that the Earth has been at or near its current oxidation state for over 3 and probably close to 4 billion years (Delano 2001), implying an atmosphere composed of neutral or perhaps even oxidized gases, such as H2O, CO2 and SO2. Such an oxidizing mixture on the early Earth would make it more difficult to make organic compounds like amino acids, by spark discharge. While most agree that the atmosphere was not reducing, on the other hand, there is no consensus that it was oxidizing either. Last year, there was a report asserting that even if the early atmosphere were dominated by CO2, the rate of escape of hydrogen from the Earth had been overestimated; therefore, more molecular hydrogen would have accumulated in the Earth's atmosphere than was previously thought. This hydrogen in turn would have allowed for some terrestrial synthesis of organic compounds (as simulated by spark discharge) albeit less efficiently than with the original Miller gas mixture.
Hydrothermal vents
In any case, if the spark discharge method of making organic molecules is not as important as it was originally thought to be, there are many other ways in which organic molecules may have formed on the early Earth. One very logical approach is to follow the hydrogen. Perhaps the most popular sites for potential organic synthesis in this vein are hydrothermal vents, and with good reason. Reducing gases emerge there, at least today, and presumably the early Earth was even more tectonically active than today, so, there would have been a great many of them early on.
The origin of life requires the formation of carbon-carbon bonds under primordial conditions 2 Miller’s experiments, in which simulating electric discharges in a reducing atmosphere of CH4, NH3, and H2O produced an aqueous solution of simple carboxylic acids and amino acids, have long been considered as one of the main pillars of the theory of a heterotrophic origin of life in a prebiotic broth. Their prebiotic significance, however, is in question, because it is now thought that the primordial atmosphere consisted mostly of an unproductive mixture of CO2, N2, and H2O, with only traces of molecular hydrogen. An alternative theory is that life had a chemoautotrophic origin.
The fixation of Co2 into living matter sustains all life on Earth, and embeds the biosphere within geochemistry. 1 The six known chemical pathways used by extant organisms for this function are recognized to have overlaps, but their evolution is incompletely understood. Here we reconstruct the complete early evolutionary history of biological carbon-fixation, relating all modern pathways to a single ancestral form. We find that innovations in carbon-fixation were the foundation for most major early divergences in the tree of life. These findings are based on a novel method that fully integrates metabolic and phylogenetic constraints. Comparing gene-profiles across the metabolic cores of deep-branching organisms and requiring that they are capable of synthesizing all their biomass components leads to the surprising conclusion that the most common form for deep-branching autotrophic carbon-fixation combines two disconnected sub-networks, each supplying carbon to distinct biomass components. One of these is a linear folate-based pathway of An external file that holds a picture, illustration, etc. Co2 reduction previously only recognized as a fixation route in the complete Wood-Ljungdahl pathway, but which more generally may exclude the final step of synthesizing acetyl-CoA. Using metabolic constraints we then reconstruct a “phylometabolic” tree with a high degree of parsimony that traces the evolution of complete carbon-fixation pathways, and has a clear structure down to the root. This tree requires few instances of lateral gene transfer or convergence, and instead suggests a simple evolutionary dynamic in which all divergences have primary environmental causes. Energy optimization and oxygen toxicity are the two strongest forces of selection. The root of this tree combines the reductive citric acid cycle and the Wood-Ljungdahl pathway into a single connected network. This linked network lacks the selective optimization of modern fixation pathways but its redundancy leads to a more robust topology, making it more plausible than any modern pathway as a primitive universal ancestral form.
The universal character of metabolism is, on the one hand, both a stronger and more striking fact of life from the vantage point of modern molecular biology than Donald Nicholson could have foreseen when he began his compilations more than a half-century ago, and on the other hand, it is a challenging regularity to express precisely. Many metabolites required by all organisms, if traced to their ultimate origin in CO2 and other inorganic inputs, require some key intermediates or reaction sequences that show no variation among known organisms. In autotrophic organisms they may be synthesized directly along these essential pathways, while in heterotrophs the dependence may be very indirect, involving multiple species and trophic exchanges, salvage pathways, and other such twists and turns, making general statements difficult in biology. Universal constraints on synthesis exist, but they require the correct unit of analysis and aggregation scale to express in rules. For this purpose, biological units such as organisms are not always the appropriate ones. For some essential functions such as carbon fixation, it would be incorrect to say that any single pathway, defined as a sufficiently complete reaction sequence to provide this function, is required by all living systems, even indirectly. Six pathways are now known to support autotrophic carbon fixation, which are in part genuinely different and independent. Yet the variations are mostly minor; all carbon fixation pathways show large overlaps of reaction sequences, and even larger homologies of reaction mechanisms and local-group chemistry. Where truly significant innovations have occurred, they appear to have been constrained to integrate within the same overall system, and therefore they feed their products back through a small standard set of precursors to anabolism and other key intermediates. For such cases, universality is not a property of any particular pathway, but must be recognized in the relations among pathways and the rules that have apparently governed the evolution of variants.
THE CARBON CYCLE 20
As already suggested, this means more than just headaches and high insurance fees for people living close to major fault lines. Plate tectonics makes possible the carbon cycle, which is essential to our planet’s habitability. This cycle is actually composed of a number of organic and inorganic subcycles, all occurring on different time scales. These cycles regulate the exchange of carbon-containing molecules among the atmosphere, ocean, and land. Photosynthesis, both by land plants and by phytoplankton near the ocean surface, is especially important since its net effects are to draw carbon dioxide from the atmosphere and make organic matter. Zooplankton, such as the forms mentioned in Chapter Two, consume much of the organic matter produced in the sunlight-rich surface. The carbonate and silicate skeletons of the marine organisms settle obligingly on the ocean floor, to be eventually squirreled away beneath the continents. Also central to the carbon cycle is the chemical weathering of silicate rocks on the continents.21 This occurs when rainwater, made acidic with dissolved carbon dioxide from the atmosphere, dissolves minerals in exposed rock. The rivers eventually carry dissolved silica (SiO2), calcium, and bicarbonate ions (derived from the carbon dioxide) to the oceans. Phytoplankton and zooplankton—and to a lesser extent, corals and shellfish— then remove these dissolved chemicals from the ocean to build their silicate and calcium carbonate skeletons. The carbon cycle is completed when the subducted carbonates are pressure-cooked deep in the crust, releasing carbon dioxide that eventually finds its way to the surface through volcanoes and springs. Negative feedback loops maintain the whole cycle in balance. Perhaps the most important stabilizing feedback is the dependence of the rate of chemical weathering on temperature. Here’s how it works: Suppose a prolonged period of large volcanic eruptions rapidly increased the amount of carbon dioxide in the atmosphere. Through the greenhouse effect, the upsurge in carbon dioxide would raise the global temperature. The higher temperature and carbon dioxide level, in turn, would speed up chemical weathering, and thus the removal of carbon dioxide from the atmosphere. Eventually, the carbon dioxide and temperature would return to their pre-eruption levels. Conversely, a drop in carbon dioxide would slow chemical weathering, allowing carbon dioxide to build up in the atmosphere. In either case, the loop comes full circle. As we’ll discuss in Chapter Four, a rise in atmospheric carbon dioxide increases plant growth. Rocks fuzzy with plants weather chemically about five times faster than bare rocks, allowing Earth to tuck carbon away under its surface all the more quickly. In other words, this accelerated weathering reinforces this stabilizing feedback loop, allowing Earth’s climate system to respond much more effectively to perturbations than could a lifeless world. Thus, plate tectonics, together with plant life, makes a planet much more nurturing for all life.
Sometimes, like in the Himalayas, continental plates thrust themselves into each other, and with nowhere to go but up, they build mountains. This is all essential for life on Earth. These processes carry carbon in and out of Earth's interior, and by doing so, regulate the amount of carbon dioxide in the atmosphere. Carbon dioxide is a greenhouse gas: too much of it, and the atmosphere traps too much heat. "The surface temperature increases and Earth eventually becomes a planet like Venus," says Jun Korenaga, a geophysicist at Yale University, US. Too little, and all the heat would escape, leaving Earth inhospitably cold. The carbon cycle therefore acts as a global thermostat, regulating itself when needed. A warmer climate also results in more rain, which helps extract more carbon dioxide out of the atmosphere.
The gas is dissolved in raindrops, which fall on exposed rock. Chemical reactions between the rainwater and rock release the carbon and minerals like calcium from the rock. The water then flows through rivers and streams, eventually reaching the ocean, where the carbon forms carbonate rocks and organic objects like seashells. The carbonate settles on the bottom of the ocean, on a tectonic plate that gets subducted, carrying the carbon into Earth's interior. Volcanoes then belch the carbon back into the atmosphere as carbon dioxide. Plate tectonics plays a part in every aspect of this cycle. Not only does subduction deliver carbon back into Earth's mantle, but tectonic activity brings fresh rock to the surface. That exposed rock is crucial for the chemical reactions that release minerals. Mountains, formed from plate tectonics, channel air upward, where it cools, condenses, and forms raindrops – which help extract carbon from the atmosphere. 21
1. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3334880/
2. http://fire.biol.wwu.edu/cmoyer/zztemp_fire/biol345_S99/huber1.pdf
3. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC1664678/
4. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC1664679/
5. https://en.wikipedia.org/wiki/Carbon_cycle
6. http://www.ams.org/journals/bull/2015-52-01/S0273-0979-2014-01471-5/S0273-0979-2014-01471-5.pdf
7. http://www.informationphilosopher.com/solutions/scientists/hartman/Metabolism.pdf
8. http://jcourtneywhite.com/wp-content/uploads/2016/09/The_Story_of_Carbon.pdf
9. https://www.sciencedaily.com/releases/2014/03/140319143904.htm
10. A privildedged plantet, Gonzalez, page 55
11. http://www.nationalgeographic.org/media/plankton-revealed/
12. http://www.mintpressnews.com/the-fabulous-history-of-plankton-and-why-our-survival-depends-on-it/44732/
13. https://www.guam.net/pub/sshs/depart/science/mancuso/apbiolecture/03_carbon/carbon.htm
14. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4283042/
15. Environmental microbiology, page 38
16. http://www.nature.com/nature/journal/v459/n7244/full/nature08057.html
17. http://creation.com/gods-micro-world
18. http://www2.cnrs.fr/en/519.htm
19. http://www.livescience.com/46250-teasing-apart-the-diatom-genome.html
20. Privileged Planet, Gonzalez, page 55
21. http://www.bbc.com/earth/story/20170111-the-unexpected-ingredient-necessary-for-life
Last edited by Admin on Fri Jun 30, 2017 1:46 pm; edited 5 times in total
