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Struktur Atom

An atom is the smallest building block of matter. Atoms are made of neutrons, protons and electrons. The nucleus of an atom is extremely small in comparison to the atom. If an atom was the size of the Houston Astrodome, then its nucleus would be the size of a pea.

Scientists use the Periodic Table in order to find out important information about various elements. Invented by Dmitri Mendeleev (1834-1907), the periodic table orders all known elements in accordance to their similarities. When Mendeleev began grouping elements, he noticed the Law of Chemical Periodicity. This law states, "the properties of the elements are periodic functions of atomic number." The periodic table is a chart that categorizes elements by "groups" and "periods." All elements are ordered by their atomic number. The atomic number is the number of protons per atom. In an atom with a neutral charge, the number of electrons equals the number of protons. The periodic table represents neutral atoms. The atomic number is typically located above the element symbol. Beneath the atomic number is the atomic mass number. Atomic mass is measured in Atomic Mass Units where 1 amu = (1/12) mass of carbon measured in grams. The atomic mass number is equal to the number of protons plus neutrons. This number is typically found beneath the element symbol. Atoms with the same atomic number, but different mass numbers are called Isotopes. Below is a diagram of a typical cell on the periodic table.

There are two main classifications in the periodic table, "groups" and "periods." Groups are the vertical columns that include elements with similar chemical and physical properties. Periods are the horizontal rows. Going from left to right on the periodic table, you will find metals, then metalloids, and finally nonmetals. The 4th, 5th, and 6th periods are called the transition metals. These elements are all metals and can be found pure in nature. They are known for their beauty and durability. The transition metals include two periods known as the lanthanides and the actinides, which are located at the very bottom of the periodic table. The chart below gives a brief description of each group in the periodic table.
Group 1A

* Known as Alkali Metals
* Very reactive
* Never found free in nature
* React readily with water

Group 2A

* Known as Alkaline earth elements
* All are metals
* Occur only in compounds
* React with oxygen in the general formula EO (where O is oxygen and E is Group 2A element)

Group 3A

* Metalloids
* Includes Aluminum (the most abundant metal in the earth)
* Forms oxygen compounds with a X2O3 formula

Group 4A

* Includes metals and nonmetals
* Go from nonmetals at the top of the column to metals at the bottom
* All oxygen form compounds with a XO2 formula

Group 5A

* All elements form an oxygen or sulfur compound with E2O3 or E2S3 formulas

Group 6A

* Includes oxygen, one of the most abundant elements.
* Generally, oxygen compound formulas within this group are EO2 and EO3

Group 7A

* Elements combine violently with alkali metals to form salts
* Called halogens, which mean "salt forming"
* Are all highly reactive

Group 8A

* Least reactive group
* All elements are gases
* Not very abundant on earth
* Given the name noble gas because they are not very reactive

The charges in the atom are crucial in understanding how the atom works. An electron has a negative charge, a proton has a positive charge and a neutron has no charge. Electrons and protons have the same magnitude of charge. Like charges repel, so protons repel one another as do electrons. Opposite charges attract which causes the electrons to be attracted to the protons. As the electrons and protons grow farther apart, the forces they exert on each other decrease.

There are different models of the structure of the atom. One of the first models was created by Niels Bohr, a Danish physicist. He proposed a model in which electrons circle the nucleus in "orbits" around the nucleus, much in the same way as planets orbit the sun. Each orbit represents an energy level which can be determined using equations generated by Planck and others discussed in more detail below. The Bohr model was later proven to be incorrect.

The "accepted" model is the quantum model. In the quantum model, we state that the electron cannot be found precisely, but we can predict the probability, or likelihood, of an electron being at some location in the atom. You should be familiar with quantum numbers, a series of three numbers used to describe the location of some object (like an electron) in three-dimensional space:

1. n: the principle quantum number, an integer value (1, 2, 3...) that is used to describe the quantum level, or shell, in which an electron resides. The principle quantum number is the primary number used to determine the amount of energy in an atom. Using one of the first important equations in atomic structure (developed by Niels Bohr), we can calculate the amount of energy in an atom with an electron at some value of n:

where:
R = Rydberg constant, a value of 1.097 X 107 per meter (m-1)
c = speed of light, 3.00 X 108 meters per second (m/s)
h = Planck's constant, 6.63 X 10 -34 Joule-seconds (J-s)
n = principal quantum number, no unit

For example, how much energy does one electron with a principle quantum number of n= 2 have?

You might ask, well, who cares? In addition to the importance of knowing how much energy is in an atom (a very important characteristic!), we can also derive, or calculate, other information from this energy value. For example, can we see this energy? The table below suggests that we can. For example, suppose that an electron starts at the n=3 level (we'll call this the excited state) and it falls down to n=1 (the ground state). We can calculate the change in energy using the equation:

Where: delta E = change in energy (Joules)
h = Planck's constant with a value of 6.63 x 10-34 (J-s)
v is frequency (seconds-1)
RH is the Rydberg constant with a value of 2.18 x 10-18J.
ni is the initial quantum number
nf is the final quantum number

Using the equation below, we can calculate the wavelength and the frequency of the energy. The wavelength and the frequency give us information about how we might "see" the energy:

Where:
v = the frequency of radiation (seconds-1)
= the wavelength (meters)
c = the speed of light with a value of 3.00 x 108 m/s in a vacuum.

Speed of light = 3.00E+08
Rydberg constant= 2.18E-18
Planck's constant= 6.63E-34

Excited state, n = 3 4 5
Ground state, n= 2 2 2
Excited state energy (in Joules) 2.42222E-19 1.363E-19 8.72E-20
Ground state energy (in Joules) 5.45E-19 5.45E-19 5.45E-19
�E= -3.02778E-19 -4.09E-19 -4.58E-19
Frequency= 4.56678E+14 6.165E+14 6.905E+14
Wavelength (nm) = 656.92 486.61 434.47

2. l ("el", not the letter "l"): the azimuthal quantum number, a number that specifies a sublevel, or subshell, in an orbital. The value of the azimuthal quantum number is always one less than the principle quantum number n. For example, if n=1, then "el"=0. If n=3, then l can have three values: 0,1, and 2. The values of l are typically not identified as "0,1,2, 3.", but are more commonly called by their historic names, "s, p, d, and f", respectively. Since the quantum numbers were discovered through the study of light and lines on an electromagnetic spectra, chemists identified the lines by their quality: sharp, principal, diffuse and fundamental. The table below shows the relationship:

Value of l Subshell designation
0 s
1 p
2 d
3 f

3. m: the magnetic quantum number. Each subshell is composed of one or more orbitals. In the study of light, it was discovered that additional lines appeared in the spectra produced when light was emitted in a magnetic field. The magnetic quantum number has values between -l and +l. When l=1, for example, m can have three values: -1, 0, and +1. Since you know from the chart above that the subshell designation for l=1 is "p", you now know that the p orbital has three components. In your study of chemistry, you will be presented with px, py, and pz. Notice how the subscripts are related to a three-dimensional coordinate system, x, y, and z. The chart below shows a summary of the quantum numbers:

Principal Quantum Number (n) Azimuthal Quantum Number (l) Subshell Designation Magnetic Quantum Number (m) Number of orbitals in subshell
1 0 1s 0 1
2 0
1 2s
2p 0
-1 0 +1 1
3
3 0
1
2 3s
3p
3d 0
-1 0 +1
-2 -1 0 +1 +2 1
3
5
4 0
1
2
3 4s
4p
4d
4f 0
-1 0 +1
-2 -1 0 +1 +2
-3 -2 -1 0 +1 +2 +3 1
3
5
7

Chemists care about where electrons are in an atom or a molecule. In the early models, we believed that electrons move like billiard balls, and followed the rules of classical physics. The graphic below attempts to show that earlier models thought that we could identify the exact path, position, velocity, etc. of an electron or electrons in an atom:

A more accurate picture is that the electron(s) reside in a "cloud" that surrounds the nucleus of the atom. This concept is shown in the graphic below:

Chemists are interested in predicting the probability that the electron will be at some particular part of this cloud. The cloud is better known as an orbital, and comes in several different types, or shapes. Atomic orbitals are known as s, p, d, and f orbitals. Each type of atomic orbital has certain characteristics, such as shape. For example, as the graphic below shows, an s orbital is spherical in shape:

On this graph, the horizontal (x) axis represents the distance from the nucleus in units of a0, or atomic units. The value of a0 is 0.0529 nanometers (nm). The vertical (y) axis represents the probability density. What you should notice is that as the electron moves farther away from the nucleus, the probability of its being found at that distance decreases. In other words, the electron prefers to hang around close to the nucleus.

The three graphics below show some other orbitals. The first graph (top left) is of a "2s" orbital. Each "s" orbital can hold two electrons in its cloud. Notice how there is a relatively high probability of an electron being near the nucleus, then some space where the probability is close to zero, then the probability increases substantially at some distance from the nucleus. The graphic at the top right shows a "2p" atomic orbital. Orbitals that are "p" orbitals can hold up to six (6) electrons in their cloud. Notice its "dumbbell" or "figure of eight" shape. At the bottom left is a "3s" orbital. Again, notice its spherical shape. Finally, at the bottom right, is a "3p" orbital.


One of the skills you will need to learn to succeed in freshman chemistry is being able to determine the electron configuration of an atom. An electron configuration is basically an account of how many electrons there are, and in what orbital they reside under "normal" conditions. For example, the element hydrogen (H) has one electron. We know this because its atomic number is one (1), and the atomic number tells you the number of electrons. Where does this electron go? All electrons start at "level" one, and tend to go into "s" orbitals first. We say that hydrogen has a "[1s1]" electron configuration. Looking at the next element on the Periodic Table --helium, or He -- we see it has an atomic number of two, so two electrons. Since " s" orbitals can hold up to two electrons, helium has an electron configuration of "[1s2]".

What about larger atoms? Let's look at carbon, with an atomic number of 6. Where do its 6 electrons go?

* First two: 1s2
* Next two: 2s2
* Last two: 2p2

We can therefore say that carbon has the electron configuration of "[1s22s22p2]".

The table below shows the subshells, the number of orbitals, and the maximum number of electrons allowed:

Subshell Number of Orbitals Maximum Number
of Electrons
s 1 2
p 3 6
d 5 10
f 7 14

The Abridged (shortened) Periodic Table below shows the electron configurations of the elements. Notice for space reasons we sometimes leave off a portion of the electron configuration. For example, look at argon (Ar), element 18. The table below shows its electron configuration as "[3s23p6]" (remembering that "p" orbitals can hold up to six (6) electrons). Its actual electron configuration is:

Ar = [1s22s22p63s23p6]

Sometimes you will see the notation: "[Ne]3s23p6", which means to include everything that is in neon (Ne, 10) plus the stuff in the "3"-level orbitals.


sumber: http://www.shodor.org/

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Weird Oxygen Bonding Under Pressure Explained

Oxygen, the third most abundant element in the cosmos and essential to life on Earth, changes its forms dramatically under pressure transforming to a solid with spectacular colors.

Eventually it becomes metallic and a superconductor. The underlying mechanism for these remarkable phenomena has been fascinating to scientists for decades; especially the origin of the recently discovered molecular cluster (O2)4 in the dense solid, red oxygen phase. Researchers from the Carnegie Institution's Geophysical Laboratory (GL), with colleagues* found that under pressure the molecules interact through their outermost electron clouds or "orbitals."

Using a newly developed synchrotron technique at HPCAT, the lab's synchrotron facility at Argonne National Laboratory, the researchers found that the interaction of these half-filled orbitals increases with increasing pressure, changing the location of the orbitals, and bringing the four oxygen molecules together to form the (O2)4 clusters at a pressure about 10,000 times the atmospheric pressure (10 gigapascals).

"The molecular interaction in oxygen revealed by this study is due to the unique fact that oxygen's outmost orbital is half-filled with two unpaired electrons," explained Yue Meng, lead author of the study at HPCAT. "As the molecules are squeezed into smaller volumes at high pressure, electrons in the orbital inevitably move about, trying to pair with electrons in the neighboring molecules."

To study the dense solid phases of oxygen, the researchers developed the high-pressure inelastic X-ray scattering technique at the Advanced Photon Source, a high-brilliance synchrotron X-ray facility at Argonne. The technique uses the synchrotron X-ray beam to probe the electronic bonding change as a diamond anvil cell subjects a sample to many hundreds of thousands of atmospheres. The researchers combined their experimental results with theoretical calculations by collaborators to further reveal that there is an increasing interactions between the neighboring (O2)4 clusters in the red-colored oxygen, providing a mechanism for forming new bonding between the oxygen clusters in still higher pressure phases.

"The behavior of oxygen at high pressure demonstrates one of the most profound effects of pressure on matter, which transforms the colorless air we breath into colorful dense solids," continued Meng. "The drastic change in the appearance of this familiar gas is due to the bonding changes in oxygen induced by high pressure."

"This is the first demonstration of how new tools can be used to probe the subtle interactions between atoms and molecules that lead to the formation of entirely new crystal structures," said Russell J. Hemley, the GL's director. "These new structures may give rise to entirely new electronic, magnetic, and other physical properties that could lead to new technologies."

The formation of molecular clusters through the anti-bonding orbital called ?* is well known in organic chemistry and the electron delocalization in cluster orbitals provides several potentials for technical applications. "It is exciting to find that oxygen forms molecular clusters under high pressure through similar mechanism and this opens a possibility for new forms of materials at high pressure with potential for technical applications," Meng concluded.

The study is published the week of August 4, in the Proceedings of the National Academy of Sciences.
Adapted from materials provided by Carnegie Institution, via EurekAlert!, a service of AAAS.

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Could Metals Help Treat Cancer?

A collaboration between chemists and biologists has made it possible to identify the effects of a new class of molecules, polyoxometalates (1), primarily composed of metals and oxygen. These molecules are very powerful inhibitors of a specific protein kinase, CK2, an enzyme that is overactive in a number of cancers. The enzyme's instrumental role in controlling cell proliferation and survival makes it an important target in the search for new medications.

These results have just been published in the journal Chemistry and Biology by chemists from the Institut de chimie moléculaire (CNRS / UPMC) and biologists from the Institut de recherche en technologies et sciences pour le vivant (iRTSV, CEA de Grenoble / CNRS / Inserm.)

Phosphorylation enzymes (2) , which include the protein kinase CK2, play a critical role in controlling cell proliferation. Deregulated protein kinase activity is implicated in a number of cancers, which has led to a recent surge in research on molecules that can inhibit the activity of these enzymes. The currently known CK2 inhibitors are all organic compounds that neutralize enzymatic activity by binding to its active site (3).

The contribution of the study carried out by the researchers at the Institut de chimie moléculaire and the Institut de recherche en technologies et sciences pour le vivant was to reveal a new class of CK2 inhibitors. The new inhibitors are inorganic molecules, polyoxometalates (POMs), primarily made up of metals (molybdenum and tungsten) and oxygen. They are the most powerful CK2 inhibitors yet discovered, working at very low (nanomolar) concentrations. In addition, the researchers showed that the mode of action of POMs, although not yet fully understood, is completely new. Unlike organic inhibitors, POMs do not bind to the active site of the enzyme.

This work opens up several areas for further research: clarifying the mechanism of action of these new molecules, finding the minimum molecular entity that can inhibit enzyme activity, and finally, given its importance in the health field, improving knowledge of how the enzyme CK2 works. In the longer term, these results could pave the way for new approaches to developing anti-cancer drugs.

Notes:

(1) Polyoxometalates are anionic inorganic metal oxide structures that have valuable catalytic properties.

(2) Phosphorylation enzymes called protein kinases can attach a phosphate group to proteins that may be inactive enzymes. The addition of the phosphate group can activate these “silent” enzymes. Protein kinases thus play a central role in controlling the activity of numerous enzymes in the cell.

(3) The active site of an enzyme is a particular region where the substrates bind together and enzymatic reactions takes place.

Journal reference:

1. Prudent et al. Identification of Polyoxometalates as Nanomolar Noncompetitive Inhibitors of Protein Kinase CK2. Chemistry & Biology, 2008; 15 (7): 683 DOI: 10.1016/j.chembiol.2008.05.018

Adapted from materials provided by CNRS.

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Global Carbon Budget: Proper Accounting Means Paying Attention To Inland Waters

Life as we know it, from the most basic microbes to our human neighbors, is carbon based. By investigating how carbon cycles through ecosystems, scientists can learn valuable information about food chains, nutrient cycling, and productivity. Because carbon dioxide is a greenhouse gas, with the ability to influence temperature, an accurate global carbon budget is needed to address climate change.

On Earth, carbon is continually cycling through terrestrial systems, inland waters, the ocean, and the atmosphere. Until little over a decade ago, when calculating the terrestrial component of the global carbon budget, inputs were limited to the ocean and the land. Because inland water bodies cover less than 1% of the Earth's surface, it was assumed that their contribution was inconsequential.

This view was recently challenged in an Ecosystems paper highlighting the findings of a National Center for Ecological Assessment and Synthesis analysis. Carried out by a team of international scientists, including Institute of Ecosystem Studies Biogeochemist Dr. Jonathan J. Cole, the paper's senior author, the group reveals that inland water bodies are important areas of terrestrial carbon transformation that deserve inclusion in global carbon cycle assessments.

While rivers were introduced into global carbon budget assessments in the late 90s, Cole and colleagues argue that current models are limited by a narrow definition of how rivers transport carbon. By depicting rivers as "pipes" that passively deliver terrestrial carbon to the sea, models fail to capture the complex transformations that occur on the journey toward the ocean. The fact is, according to the authors, that half of the terrestrial carbon entering inland waters is destined for a fate outside of the ocean's salty shores.

Where does the remaining terrestrial carbon go? Approximately 40% is returned to the atmosphere as CO2 and 12% is stored in sediments. This holds true across a range of inland systems, from lakes and rivers to reservoirs and wetlands. Carbon budgets that are based on the passive pipe view are flawed because in-system transformations fall off the balance sheets. Even if models were adjusted to embrace a more dynamic view of river inputs, they would need further amending to include the true range of inland waters.

Take, for instance, the role played by lakes and reservoirs. By burying carbon in their sediments, lakes serve as important regional carbon stores. In aggregate, lakes play a significant role in the global carbon budget. On an annual basis, they bury 40% as much carbon as the ocean. Reservoirs, which are steadily increasing in number, bury more organic carbon than all natural lake basins combined and exceed oceanic organic carbon burial by more than 1.5-fold.

These findings debunk the concept that inland waters are inconsequential when accounting for the global carbon budget; instead they are places of complex and active carbon transformation. The take home message from the authors: "Continental hydrologic networks, from river mouths to the smallest upstream tributaries, do not act as neutral pipes-- they are active players in the carbon cycle despite their modest size."

As global carbon budget models move from static boxes to dynamic flows, future models should take into account the myriad of ways that inland waters contribute to the carbon cycle. In many cases, these aquatic systems are biogeochemical "hot spots" within the terrestrial landscape with contributions that are significant at regional to global scales.

This paper was made possible through the joint effort of a NCEAS working group that included: J. J. Cole, Y. T. Prairie, N. F. Caraco, W. H. McDowell, L. J. Tranvik, R. G. Striegl, C. M. Duarte, P. Kortelainen, J. A. Downing, J. J. Middelburg, and J. Melack.
Adapted from materials provided by Institute of Ecosystem Studies, via EurekAlert!, a service of AAAS.

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U.S. Pacific Coast Waters Turning More Acidic

An international team of scientists surveying the waters of the continental shelf off the West Coast of North America has discovered for the first time high levels of acidified ocean water within 20 miles of the shoreline, raising concern for marine ecosystems from Canada to Mexico.

Researchers aboard the Wecoma, an Oregon State University research vessel, also discovered that this corrosive, acidified water that is being "upwelled" seasonally from the deeper ocean is probably 50 years old, suggesting that future ocean acidification levels will increase since atmospheric levels of carbon dioxide have increased rapidly over the past half century.


Results of the study were just published in Science Express.

"When the upwelled water was last at the surface, it was exposed to an atmosphere with much lower CO2 (carbon dioxide) levels than today's," pointed out Burke Hales, an associate professor in the College of Oceanic and Atmospheric Sciences at Oregon State University and an author on the Science study. "The water that will upwell off the coast in future years already is making its undersea trek toward us, with ever-increasing levels of carbon dioxide and acidity.

"The coastal ocean acidification train has left the station," Hales added, "and there not much we can do to derail it."

Scientists have become increasingly concerned about ocean acidification in recent years, as the world's oceans absorb growing levels of carbon dioxide from the atmosphere. When that CO2 mixes into the ocean water, it forms carbonic acid that has a corrosive effect on aragonite -- the calcium carbonate mineral that forms the shells of many marine creatures.

Certain species of phytoplankton and zooplankton, which are critical to the marine food web, may also be susceptible, the scientists point out, although other species of open-ocean phytoplankton have calcite shells that are not as sensitive.

"There is much research that needs to be done about the biological implications of ocean acidification," Hales said. "We now have a fairly good idea of how the chemistry works."

Increasing levels of carbon dioxide in the atmosphere are a product of the industrial revolution and consumption of fossil fuels. Fifty years ago, atmospheric CO2 levels were roughly 310 parts per million -- the highest level to that point that the Earth has experienced in the last million years, according to analyses of gas trapped in ice cores and other research.

During the past 50 years, atmospheric CO2 levels have gradually increased to a level of about 380 parts per million.

These atmospheric CO2 levels form the beginning baseline for carbon levels in ocean water. As water moves away from the surface toward upwelling areas, respiration increases the CO2 and nutrient levels of the water. As that nutrient-rich water is upwelled, it triggers additional phytoplankton blooms that continue the process.

There is a strong correlation between recent hypoxia events off the Northwest coast and increasing acidification, Hales said.

"The hypoxia is caused by persistent upwelling that produces an over-abundance of phytoplankton," Hales pointed out. "When the system works, the upwelling winds subside for a day or two every couple of weeks in what we call a 'relaxation event' that allows that buildup of decomposing organic matter to be washed out to the deep ocean.

"But in recent years, especially in 2002 and 2006, there were few if any of these relaxation breaks in the upwelling and the phytoplankton blooms were enormous," Hales added. "When the material produced by these blooms decomposes, it puts more CO2 into the system and increases the acidification."

The research team used OSU's R/V Wecoma to sample water off the coast from British Columbia to Mexico. The researchers found that the 50-year-old upwelled water had CO2 levels of 900 to 1,000 parts per million, making it "right on the edge of solubility" for calcium carbonate-shelled aragonites, Hales said.

"If we're right on the edge now based on a starting point of 310 parts per million," Hales said, "we may have to assume that CO2 levels will gradually increase through the next half century as the water that originally was exposed to increasing levels of atmospheric carbon dioxide is cycled through the system. Whether those elevated levels of carbon dioxide tip the scale for aragonites remains to be seen.

"But if we somehow got our atmospheric CO2 level to immediately quit increasing," Hales added, "we'd still have increasingly acidified ocean water to contend with over the next 50 years."

Hales says it is too early to predict the biological response to increasing ocean acidification off North America's West Coast. There already is a huge seasonal variation in the ocean acidity based on phytoplankton blooms, upwelling patterns, water movement and natural terrain. Upwelled water can be pushed all the way onto shore, he said, and barnacles, clams and other aragonites have likely already been exposed to corrosive waters for a period of time.

They may be adapting, he said, or they may already be suffering consequences that scientists have not yet determined.

"You can't just splash some acid on a clamshell and replicate the range of conditions the Pacific Ocean presents," Hales said. "This points out the need for cross-disciplinary research. Luckily, we have a fantastic laboratory right off the central Oregon coast that will allow us to look at the implications of ocean acidification."

The study, funded by the National Oceanic and Atmospheric Administration (NOAA) and the National Aeronautics and Space Administration (NASA), was the first in a planned series of biennial observations of the carbon cycle along the West Coast of the continent. In addition to Hales, principal investigators for the study included Richard A. Feely and Christopher Sabine of the NOAA Pacific Marine Environmental Laboratory; J. Martin Hernandez-Ayon, the University of Baja California in Mexico; and Debby Ianson, of Fisheries and Oceans Canada, Sidney, B.C.
Adapted from materials provided by Oregon State University.

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Microbe Diet Key To Carbon Dioxide Release

As microbes in the soil break down fallen plant matter, a diet "balanced" in nutrients appears to help control soil fertility and the normal release of the greenhouse gas carbon dioxide into the atmosphere.

When plants drop their leaves, stems and twigs, this organic matter slowly becomes part of the soil as a result of decomposition, which is facilitated by bacteria and other microbes. This process adds plant nutrients to the soil and releases carbon dioxide into the atmosphere.

Duke University scientists found the proportion of nitrogen to carbon in this organic matter determines how much nitrogen becomes available to plants in the soil and how much carbon dioxide is released into the atmosphere. Their study also yielded a universal mathematical formula that can predict the decomposition process anywhere in the world.

The results of the Duke analysis were published Aug. 1 in the journal Science.

"For the first time, we have been able to demonstrate that the pattern of carbon dioxide release into the atmosphere through decomposition is governed by the same properties everywhere, from the Arctic Circle to tropical rain forests," said first author Stefano Manzoni, a Ph.D. candidate in civil and environmental engineering who works in the laboratory of senior scientist Amilcare Porporato, associate professor of civil engineering in Duke's Pratt School of Engineering. "This provides a mathematical way of describing a critical natural process."

During decomposition, microbes digest fallen organic matter from plants and slowly break it down. Two of the important byproducts of this process are mineral nitrogen and carbon dioxide. Nitrogen is an essential nutrient for both plants and microbes, and once it becomes mineralized, it becomes available for plants to use.

Carbon -- the most abundant element in plants and organic matter -- is released into the atmosphere in the form of carbon dioxide, one of many of the so-called greenhouse gases implicated in global warning. This carbon dioxide release is known as respiration.

"One of the key findings of this study is that microbes can adapt and do fairly well in a nutrient-poor environment," Porporato said. "When their diet is lacking in nitrogen, microbes tend to react by releasing more carbon dioxide into the air and taking in less mineral nitrogen from the soil. So plants can get the much-needed mineralized nitrogen earlier in the decomposition process from the fallen organic matter."

However, he pointed out, the earlier availability of mineral nitrogen for plant use comes at a risk: nitrogen in this form in the soil becomes more vulnerable to rain, which can wash it away or leach it deeper into the soil. This would be especially true if the rainfall events are particularly heavy, as has been predicted in some climate-change models.

Maintaining enough soil nitrogen is important in both native ecosystems and in farms and orchards, the scientists said.

"Nitrogen is the element that most limits plant growth around the world," said co-author Rob Jackson, Duke professor of biology and environmental sciences. "Our work should help predict how much nitrogen becomes available when organic matter is added to the soil, either naturally or through added mulches and manures."

For the analysis, Manzoni assembled a database of more than 2,800 samples of decomposing plant matter from locations around the world in a wide spectrum of climates. As he studied decomposition across these sites, he found similar patterns of nitrogen release and respiration no matter what the climate was like.

"A diet rich in carbon causes microbes to release more carbon into the atmosphere in the form of carbon dioxide as they strive to maintain the healthy balance between nitrogen and carbon in their diet," Manzoni said. "For this reason, if more carbon is added to the soil in the form of plant residues, the microbes would then just pump out more carbon in response."

The research team plans to use the same approach to better understand the roles of other nutrients in the decomposition cycle.

The research was funded by the U.S. Department of Energy and the National Science Foundation. John Trofymow of the Canadian Forest Service was also a member of the team. Much of the data used in the current analysis came from the Long-Term Intersite Decomposition Experiment (LIDET), a partnership of the U.S Forest Service, Oregon State University and the U.S. Department of Forest Science, as well as the Canadian Intersite Decomposition Experiment (CIDET).
Adapted from materials provided by Duke University.

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