Thursday, October 16, 2008

Microbes - Our Friendly Allies

by Richard Chew

I've read some materials on rose growing and I learned that we are blessed with God's micro creation that we cannot take them for granted. They are essentials for cultivating healthy plants. They are our friendly allies.
It is not necessary to know the details of what microbes do. But more importantly what is necessary to get these friendly allies to work favourably for your plants.

These are some few suggestions you can use.

1. Keep your soil aerated. If earthworms are numerous in your soil, it should provide sufficient aeration. If the soil becomes compacted due to continuous pouring rain, then it is necessary to fork it to improve water drainage. Best indication of good soil aeration, is that bubble surfaces when watering. Aeration is important because Bacteria utilises Nitrogen (N2) from atmospheric air and convert them into "food" for other micro-organism in the soil.

2. Keep soil fertilised with organic manure. As the organic manure decomposes, these microbes will gain the energy to convert Nitrogen gas (N2) from the air into the form that the plant can use.

However there are some special situations that we need to take some pre-cautions. If we understand how these microbes function and apply some counter measures, then it is highly likely we can help sustain high nitrogen production cycle that benefits your plant.

The following are some situations that may limit the cycle of Nitrogen production.

1. Excessive rain - that clogs aeration in soil, thus lack of Nitrogen gas in the soil impedes the rate of decomposition (lower rate of bacteria activity)

2. Lack of sunlight - Lack of sun light will lower photosynthesis activity, thus cause an imbalance of the symbiotic activity of Nitrogen Fixing Bacteria that resides at the roots nodules. The bacteria continue to consume "food" stored at the roots that is supposedly supplied from the photosynthesis process. This cause a depletion in carbon component in the plant. If left unattended the plant condition may deteriorate.

3. Low Nitrogen ratio fertiliser - If low nitrogen material is used for fertilisation (example tree leaves, eggshells or any materials that decompose slowly), it may cause temporary shortage of nitrogen as the microbes draw too much nitrogen from the soil to digest the low-nitrogen material (decompose).

The above diagram illustrate the complete nitrogen cycle. The plant cannot take in nitrogen from the atmosphere directly. It relies on bacteria to convert them (through multiple stages) into a form that can be absorb into the plant. As illustrated above, the end cycle is Nitrates (NO3-) that is assimilated into the plant roots.

Ammonification Phase

N2 + 8H+ + 8e− + 16 ATP → 2NH3 + H2 + 16ADP + 16 Pi

Although ammonia (NH3) is the direct product of this reaction, it is quickly protonated into ammonium (NH4+).

Nitrification Phase

NH3 + CO2 + 1.5 O2 + Nitrosomonas → NO2- + H2O + H+

NO2- + CO2 + 0.5 O2 + Nitrobacter → NO3-

Nitrifying bacteria converts ammonia to nitrite (NO2-) and subsequently converts nitrite to nitrate (NO3-) which shall be assimilated by the plant as nutrient. To accomplish this task, the bacteria needs CO2 and O2 from the atmospheric air. This explains the importantance of having good soil aeration to ensure higher nitrogen production for the plant roots.

This is why I like to water plants in the morning and also in the evening, always twice daily. Obviously apart from the main purpose for moisting the soil, the other important purpose is to flushed out the "burned" air so that more fresh CO2 and O2 replaces the pores in the soil.

The presence of earthworms in soil helps keep the soil aerated and its worm casting contains Nitrate (NO2-) and bacteria too, thus increase the nitrifying acitivities in the soil.

Another important information is that these bacteria also involved in the formation of soil aggregation. They produce organic compounds called polysaccharides (complex carbohydrates ; Cn (H2O)n-1 where n is usually large number between 200 and 2500), that binds soil particles together in aggregates. These aggregates can vary in size, and they do not necessary fit together thus creating spaces and pores within and between the soil. These spaces and pores are essential for storing air and water, microbes and nutrients in the soil.

I hope by now you will appreciate these lowly creatures. Though they may seemed insignificant, they largely contributes to our food chain.

In case you wish to understand a little bit more, please refer to the useful links below that explains what Bacterias do in the soil. I have extracted this piece of information from the US Department of Agriculture and posted it in this blog.

Wednesday, October 15, 2008


Extracted from


Bacteria are tiny, one-celled organisms – generally 4/100,000 of an inch wide (1 µm) and somewhat longer in length. What bacteria lack in size, they make up in numbers. A teaspoon of productive soil generally contains between 100 million and 1 billion bacteria. That is as much mass as two cows per acre.

Figure 1: A ton of microscopic bacteria may be active in each acre of soil.Credit: Michael T. Holmes, Oregon State University, Corvallis.

Figure 2: Bacteria dot the surface of strands of fungal hyphae.Credit: R. Campbell. In R. Campbell. 1985. Plant Microbiology. Edward Arnold; London. P. 149. Reprinted with the permission of Cambridge University Press.

Bacteria fall into four functional groups. Most are decomposers that consume simple carbon compounds, such as root exudates and fresh plant litter. By this process, bacteria convert energy in soil organic matter into forms useful to the rest of the organisms in the soil food web. A number of decomposers can break down pesticides and pollutants in soil. Decomposers are especially important in immobilizing, or retaining, nutrients in their cells, thus preventing the loss of nutrients, such as nitrogen, from the rooting zone.

A second group of bacteria are the mutualists that form partnerships with plants. The most well-known of these are the nitrogen-fixing bacteria. The third group of bacteria is the pathogens. Bacterial pathogens include Xymomonas and Erwinia species, and species of Agrobacterium that cause gall formation in plants. A fourth group, called lithotrophs or chemoautotrophs, obtains its energy from compounds of nitrogen, sulfur, iron or hydrogen instead of from carbon compounds. Some of these species are important to nitrogen cycling and degradation of pollutants.


Bacteria from all four groups perform important services related to water dynamics, nutrient cycling, and disease suppression. Some bacteria affect water movement by producing substances that help bind soil particles into small aggregates (those with diameters of 1/10,000-1/100 of an inch or 2-200µm). Stable aggregates improve water infiltration and the soil’s water-holding ability. In a diverse bacterial community, many organisms will compete with disease-causing organisms in roots and on aboveground surfaces of plants.


Nitrogen-fixing bacteria form symbiotic associations with the roots of legumes like clover and lupine, and trees such as alder and locust. Visible nodules are created where bacteria infect a growing root hair (Figure 4). The plant supplies simple carbon compounds to the bacteria, and the bacteria convert nitrogen (N2) from air into a form the plant host can use. When leaves or roots from the host plant decompose, soil nitrogen increases in the surrounding area.

Nitrifying bacteria change ammonium (NH4+) to nitrite (NO2-) then to nitrate (NO3-) – a preferred form of nitrogen for grasses and most row crops. Nitrate is leached more easily from the soil, so some farmers use nitrification inhibitors to reduce the activity of one type of nitrifying bacteria. Nitrifying bacteria are suppressed in forest soils, so that most of the nitrogen remains as ammonium.

Denitrifying bacteria convert nitrate to nitrogen (N2) or nitrous oxide (N2O) gas. Denitrifiers are anaerobic, meaning they are active where oxygen is absent, such as in saturated soils or inside soil aggregates.

Actinomycetes are a large group of bacteria that grow as hyphae like fungi (Figure 3). They are responsible for the characteristically “earthy” smell of freshly turned, healthy soil. Actinomycetes decompose a wide array of substrates, but are especially important in degrading recalcitrant (hard-to-decompose) compounds, such as chitin and cellulose, and are active at high pH levels. Fungi are more important in degrading these compounds at low pH. A number of antibiotics are produced by actinomycetes such as Streptomyces.

Figure 3: Actinomycetes, such as this Streptomyces, give soil its "earthy" smell.Credit: No. 14 from Soil Microbiology and Biochemistry Slide Set. 1976. J.P. Martin, et al., eds. SSSA, Madison, WI

Figure 4: Nodules formed where Rhizobium bacteria infected soybean roots.Credit: Stephen Temple, New Mexico State University


Various species of bacteria thrive on different food sources and in different microenvironments. In general, bacteria are more competitive when labile (easy-to-metabolize) substrates are present. This includes fresh, young plant residue and the compounds found near living roots. Bacteria are especially concentrated in the rhizosphere, the narrow region next to and in the root. There is evidence that plants produce certain types of root exudates to encourage the growth of protective bacteria.

Bacteria alter the soil environment to the extent that the soil environment will favor certain plant communities over others. Before plants can become established on fresh sediments, the bacterial community must establish first, starting with photosynthetic bacteria. These fix atmospheric nitrogen and carbon, produce organic matter, and immobilize enough nitrogen and other nutrients to initiate nitrogen cycling processes in the young soil. Then, early successional plant species can grow. As the plant community is established, different types of organic matter enter the soil and change the type of food available to bacteria. In turn, the altered bacterial community changes soil structure and the environment for plants. Some researchers think it may be possible to control the plant species in a place by managing the soil bacteria community.

Sunday, October 12, 2008


I extracted this from NASA Goddard Space Flight Center site. I find this discovery interesting as it gives new insight about diffuse light on the efficiencies of photosynthesis rate.


New NASA-funded research shows that when the atmosphere gets hazy, like it did after the eruption of Mt. Pinatubo in the Philippines in June 1991, plants photosynthesize more efficiently, thereby absorbing more carbon dioxide from the atmosphere.

When Mount Pinatubo erupted, scientists noticed the rate at which carbon dioxide (CO2) filled the atmosphere slowed down for the next two years. Also during 1992 and 1993, ash and other particles from the volcano created a haze around the planet and slightly reduced the sunlight reaching Earth's surface and made the sun's radiation less direct and more diffuse.

Many scientists previously thought the reduction in sunlight lowered the Earth's temperature and slowed plant and soil respiration, a process where plants and soil emit CO2. But this new research shows that when faced with diffuse sunlight, plants actually become more efficient, drawing more carbon dioxide out of the air.

"There is evidence indicating that the drop in the atmospheric CO2 growth rate was probably too big to be explained by a reduction in respiration alone," said the study's lead author, Lianhong Gu, a researcher at the University of California Berkeley's Department of Environmental Science, Policy and Management.

Gu added that the respiration rates of plants and soil are sensitive to temperature changes. But "in order to explain the drop in atmospheric growth rate of CO2, we would need an average drop in global temperatures of about 3.6 degrees Fahrenheit (2° C), but the temperatures only dropped by about one degree (0.9) Fahrenheit (0.5°C) globally."

Plants take in carbon dioxide during photosynthesis in the day, and release it during respiration at night. But they don't necessarily photosynthesize and respire at the same rates. Since decreased plant and soil respiration could not explain the drop in carbon dioxide entering the atmosphere in 1992 and 1993, Gu and his colleagues deduced that enhanced photosynthesis by plants must be involved.

After Mount Pinatubo erupted, while overall solar radiation was reduced by less than five percent, data showed a reduction of direct radiation by as much as 30 percent. So, instead of direct light, the sun's rays were reaching leaves after colliding with particles in the air.

"Diffuse radiation has advantages for plants," Gu said. That's because when plants receive too much direct light, they become saturated by radiation and their ability to photosynthesize levels off. In the layers of leaves from top to bottom, called the plant canopy, only a small percentage of the leaves at the top actually get hit by direct light. In the presence of diffuse light, plants photosynthesize more efficiently and can draw more than twice as much carbon from the air than when radiated by direct light.

Gu and his colleagues tested the CO2 uptake in various plant ecosystems around the world-including Aspen forests, mixed deciduous forests, Scots pine forests, tallgrass prairies, and a winter wheat field-based on the amount of solar radiation striking the leaves. From these analyses, they generated parameters necessary for evaluating impacts of the Pinatubo eruption. On clear days following the eruption, they found that in all of the ecosystems, photosynthesis increased under the diffuse light.

While large volcanic eruptions are rare, this research has big implications for more regular phenomena such as the effects of aerosols and clouds on an ecosystem's ability to pull carbon from the atmosphere. Aerosols, or microscopic particles like soot or black carbon in the air, occur naturally but have also been increasing due to human activities since the industrial revolution. Gu's research indicates that the maximum uptake of carbon dioxide by plant ecosystems occurs when cloud cover is about 50 percent.

The research will be presented at a poster session of the American Geophysical Union (AGU) Fall Meeting in San Francisco, Calif. on December 14, 2001. A paper will be published soon in the Journal of Geophysical Research.

Aside from NASA, the study was also funded by the National Oceanic and Atmospheric Administration (NOAA), the Department of Energy, and other organizations, through the FLUXNET program.

Editor's Note: AGU Title, Time and Location"Roles of Volcanic Eruptions, Aerosols and Clouds in Global Carbon Cycle"Friday, December 14, 2001, 8:30 AM, Moscone Center Hall