[Michaelangelica]

SOIL MICROBOLOGY: A PRIMER

By Vern Grubinger
Vegetable and Berry Specialist
University of Vermont Extension

Although it may not be obvious, healthy soils are chock-full of living organisms. Some are visible to the naked eye, like earthworms, beetles, mites and springtails, but the majority of soil-dwellers are very, very small. They’re also very, very important to soil fertility.

Just a few grams of soil, less than a teaspoonful, may contain hundreds of millions to billions of microbes. Not only is the total number of microorganisms in fertile soil quite high, but together, they weigh a lot, too. Soil microbial biomass can range from several hundred to thousands of pounds per acre.

By far, the most numerous microbes in soil are bacteria, which have just one cell. Also abundant are fungi, which produce long, slender strings of cells called filaments, or hyphae. The actinomycetes are in-between these two organisms. They are advanced bacteria that can form branches like fungi. It’s the actinomycetes that give soil its characteristic earthy smell. Fungi and actinomycetes are good at starting the decomposition of organic residues, working on materials that are tough to break down. Bacteria finish the job by eating the more digestible ingredients.

Many other microbes can be found in smaller numbers in soil, including algae, cyanobacteria (often called blue-green algae), and protozoa (one-celled organisms that decompose organic materials and also consume bacteria). Nematodes are microscopic roundworms; some of these are beneficial and some are plant parasites.

Soil Microbilogy: A Primer

May 30, 2006
Essential organism -- from peat bogs -- involved in global climate change is finally isolated for study
By Krishna Ramanujan

Among the unusual life forms found in peat bogs are carnivorous pitcher plants and methanogens, methane-producing single-celled organisms that live in oxygen-free environments. But efforts to take methanogens from acidic peat bogs and then isolate and culture them in the laboratory under peat bog conditions have been unsuccessful -- until now.

In a recent article in Nature Online, Cornell researchers published their methods for creating an acidic culture medium that isolated methanogens and allowed the organisms to thrive in a test tube. This will allow researchers to study methane-producing organisms and to better understand how they function in peat bogs and how they might respond to global climate change.

Indeed, methanogens play an important role in global climate because they are the largest natural sources of atmospheric methane -- a heat-trapping greenhouse gas 21 times more potent than carbon dioxide. Northern peat bogs hold one-third of the carbon fixed in the world's soils, the. . .

. . .
Even though methanogens dominate bogs, researchers have been unable to take them from the bog and then grow them in the laboratory. Braüer, Zinder and their colleagues used an antibiotic called rifampicin that killed off the bacteria in the sample but spared the methanogens. The methane-producers belong to a kingdom called Archaea, separate from bacteria and not bothered by most antibiotics.

Methanogens study

[Michaelangelica]

transect points: Home Grown Biofertilizer

Saturday, February 24, 2007
Home Grown Biofertilizer


The role that soil microbes (archaea, bacteria, and fungi) play in soil nutrient availability is an interesting area, one where we have much to explore. Biofertilizers are increasingly available commercially, meaning those of us outside the academic community will have increasing opportunity to conduct our own reseach

See here for complete article
transect points: Home Grown Biofertilizer
I posted this in response to a the above 'transect points' blog

michaelangelica said...

I vaguely recall a Japanese study where they found a bacteria that made phosphorus available.
I think they said that their volcanic soils contain a lot of phosphorus but it is not readily available to plants. They were interested in Australian technology with making super phosphate applied to farms more available.

Australian soils are phosphate poor. Most natives react very badly (die) to phosphorus because they have evolved in a low phosphorus environment.
What happens if the Japaneses phosphorus-making-available "wee beastie" visits Australia? How would the native plants feel about that I wonder?

It seems we need to spend a lot more $ working out the different "suites" of 'critters' that live and have evolved in different parts of the world.
I am worried that throwing about commercial 'wee beastie' mixes might kill or endanger native bacteria, fungi etc before we have even managed to give them a name - let alone work out what they do.

I guess whenever we garden we destroy as well as create.

In housing estates popping up locally on virgin soil developers are required to collect native seed growing in the proposed development area, propagate it and replant it when the houses are up.
No one has yet thought of asking what the amazing soil zoo under their feet contains.
RIP

[Michaelangelica]

All subsequent work has served to underpin the fundamental importance of the vast masses of soil micro-organisms in plant nutrition and growth, and particularly that of the mycorrhiza-forming soil fungi.

"It is well known that mycorrhizae can benefit the growth and health of plants, but it is not widely known or appreciated just how critical and normal this association is to the well-being of plants, especially in disturbed ecosystems" (Dr. Robert G. Linderman, USDA-ARS, Horticultural Crops Research Laboratory).

What also is not very widely known is how chemical fertilizers and pesticides can damage or even destroy the essential soil fungi, as well as the rest of the vast web of soil microlife so vital to soil and crop health. See what Dr. Elaine Ingham has to say about this.

What is the mycorrhizal association? Simply put, in a healthy soil plant roots are invaded by a friendly soil fungus; the fungus actually feeds the plant, and in return the plant feeds the fungus the products of the green leaf which the fungus is unable to make for itself. It is a very ancient and widespread arrangement, long overlooked after its initial discovery mainly because the plant pathologists of the time, with their orientation towards disease, saw the fungal invasion as a pest attack.

Long out of print, "Trees and Toadstools" by Dr. Rayner is an excellent introduction to the subject. With her husband and co-worker, Professor W. Neilson-Jones, she also wrote an account of the work with mycorrhizas at Wareham: "Problems in Tree Nutrition -- An account of researches concerned primarily with the mycorrhizal habit in relation to forestry and with some biological aspects of soil fertility" (Faber and Faber, 1944), also long out of print, though we hope eventually to add it to this library.

Trees and Toadstools - Introduction

[maikeru]

Lovely links, Michaelangelica. A few on nitrogen fixation by "wee beasties":

Nitrogen fixation (technical)
nitrogen fixation: Definition and Much More from Answers.com
NITROGEN FIXATION (technical)
Biological Nitrogen Fixation

Cyanobacteria and soil ecology:

Biofertilizers
CAT.INIST
Bio-fertilizers for Coffee Plantations (INeedCoffee.com)
Capitol Reef - Cryptobiotic Soil
Plant Ecology Lab, Soil Crusts, Archbold Biological Station, 9 May 2002, Fred E. Lohrer. Added PDF file link 31 May 2002.
Cyanobacteria

I think the topics of nitrogen cycling and nitrogen fixation are especially pertinent, because findings often state that biochar/terra preta soils are usually very rich in nitrogen.

I wish I could link to an online version of one of my old textbooks: Brock's Biology of Microorganisms. It has a lot of useful general info on soil microbes as well as specifics on their biochemistry and interactions with plants.

Edit: Now that I mentioned it, I searched to see what is available online and Brock's isn't free on the net, but it does have useful weblinks on the textbook's website for chapter headings and related topics:

Microorganisms and Microbiology

Maybe useful for those willing to check out further web resources?

Molecular Biology of the Cell by Alberts et al.:

Molecular Biology of the Cell

Online and searchable! Another one of my textbooks which I always keep by my desk. Useful for microbial technical details.

[Michaelangelica]

Carbon 'released, not stored' by soil
Tuesday, 20 March 2007
Wagdy Sawahel
SciDev.Net
Carbon 'released, not stored' by soil
Soils may not always act as carbon sinks, a new study suggests
Image: Derek Jensen

CAIRO: Rising levels of carbon dioxide in the air may turn soil from a potential carbon sink into an emission source by stimulating microbes to release carbon dioxide, according to a new study.

This article
Carbon 'released, not stored' by soil | COSMOS magazine
seems at odds with this one
Potential responses of soil organic carbon to global environmental change -- Trumbore 94 (16): 8284 -- Proceedings of the National Academy of Sciences

SOM is difficult to study because it is a complex mixture of substances having turnover rates that range from days to millennia.
The average global turnover time for soil organic carbon (to 1-m depth) was estimated as 32 years by Raich and Schlesinger (34), who divided the total C stock in soils by the average CO2 flux from soil (corrected for root respiration contribution).
Turnover times varied from 14 years to 400 years for different ecosystems in their study. Radiocarbon measurements of bulk soil C, however, often show that the average age of C in soils is several hundred to several thousand years (35-38).
Both results are explained if SOM contains components that turn over slower and faster than the several-decade average.

[malcolmf]

Originally Posted by Michaelangelica

SOM is difficult to study because it is a complex mixture of substances having turnover rates that range from days to millennia ... results are explained if SOM contains components that turn over slower and faster than the several-decade average.

This is a key point in relation to your beasties, Michael. Models of the soil carbon cycle (e.g. Colorado Uni's Century) usually allow for such pools as fast (1 year), slow (decades) and stable (centuries / millennia) turnover rates. However, even these are approximations: some papers on mycorrhizae suggest their turnover time can be as little as five days, as compared to the glomalin they produce which seems to join the slow pool.

The headline is that, once creatures get hold of carbon, it is as good as gone, back to the air. This implies a trade-off between the two main goals of carbon burial, namely removal from the air and agricultural productivity. The former does not want creatures to access the carbon, the latter does. We have to examine our motivations for making terra preta, and the two camps might choose very different methods as a result. I suggest that atmospheric goals might require high-tech, high-volume, highly recalcitrant carbon while soil goals might require something much closer to Amazonian practices or RBlack's carbon-compost approach.

Your history is in compost, isn't it? How do you feel about the potential conflict of goals between atmosphere and soil?

M

[Michaelangelica]

Still thinking
I need more information

Something else to consider:-

Triclosan, Triclocarban Concern
transect points: Triclosan, Triclocarban Concern

transect points: Triclosan Update

“We’ve been using triclocarban for almost half a century at rates approaching 1 million pounds per year, but we have essentially no idea of what exactly happens to the compound after we flush it down the drain,”
. . .
“Along with its chemical cousin triclosan, the antimicrobial compound triclocarban should be added to the list of polychlorinated organic compounds that deserve our attention due to unfavorable environmental characteristics, which include long-term persistence and potential bioaccumulation.

Triclocarban, for example, has an estimated half-life of 1.5 years in aquatic sediments. Do the potential benefits of antimicrobial products outweigh their known environmental and human health risks? This is a scientifically complex question consumers, knowingly or unknowingly, answer to everyday in the checkout line of the grocery store,” said Dr. Halden.

Beyond Pesticides

If you look carefully you will find them in a surprising range of products including antibacterial soaps, deodorants, toothpaste, mouthwash, even dish soap and cutting boards. You won’t have to look far; over 70% of the liquid soaps contain Triclosan.

A Better Way To Clean » Blog Archive » Take a Stand on Triclosan

More than a million pounds of antimicrobial chemicals from soap and other products flow into the nation's sewers every year. Do these compounds pose a risk?
. . .
New data puncture that conclusion: 50 percent of triclosan and 76 percent of triclocarban remain unchanged by aerobic and anaerobic digestion in a typical wastewater facility,
. . .
Overall, Halden's team estimates that more than 100,000 pounds of triclosan and over 300,000 pounds of triclocarban are spread on the ground as sludge each year in the United States,

Recent studies show that triclosan acts like an antibiotic in the way it kills bacteria and may contribute to the development of antibiotic resistant bacteria.

Chemically, triclosan is almost the same as some of the most toxic chemicals on earth: dioxins, PCB's, and Agent Orange. Its manufacturing process may produce dioxin, a powerful hormone-disrupting chemical with toxic effects in the parts per trillion (one drop in 300 Olympic-sized swimming pools!).

Triclosan is a chlorophenol, a class of chemicals suspected of causing cancer in humans
. . .
Triclosan is stored in body fat. "It can accumulate to toxic levels,

http://articleaware.com/Details.aspx...ywords=ethanol
American Scientist Online - Persistently Clean?...

[Michaelangelica]

Wee beasties flex a bit of muscle

A collection of blind crustaceans and scorpion-like animals has stopped the development of a multi-billion-dollar iron mine in Western Australia. The state's environment agency rejected the project for fear the tiny cave-dwellers would become extinct.

The Mesa A / Warramboo iron ore mining project was proposed by Robe River, part of mining giant Rio Tinto.
But Western Australia's Environmental Protection Authority (EPA) rejected the proposal after it unearthed troglobitic animals on the site, near Pannawonica, in the Pilbara region of the state.

The tiny animals are a collection of crustaceans, worms and scorpion-like critters that live entirely in the dark parts of caves. Troglobite is a term used to describe an animal that has adapted to life in total darkness and may have no eyes or pigmentation, using feelers to negotiate their dark habitat.
They cannot survive outside their pitch-dark world because ultraviolet light is lethal to them – even short exposure to sunlight can be fatal.

An EPA report (pdf format) into the project found 11 species of troglobitic animals in the area, some of which were new species and unknown elsewhere. The report's authors said mining would kill off at least five of these species.

Tiny blind critters halt billion-dollar mine - earth - 30 March 2007 - New Scientist Environment

[Michaelangelica]

Gardening cures deprsssion!?

Mycobacterium vaccae, a harmless bacteria normally found in dirt, has been found to stimulate the immune system of mice and boost the production of serotonin, a mood-regulating brain chemical.

The bacterium has already been successfully used in people as a vaccine against tuberculosis. It is also being tested as a treatment for cancer patients and in asthma sufferers, as a way to control the allergic reaction and help 'rebalance' the immune system.

How gardening could cure depression | COSMOS magazine

[Michaelangelica]

I found this fascinating
Japan has its own "wee beastie" that make phosphorus available to plants!
Indigenous microorganisms which solubilize mineral bound
phosphates by the excretion of chelating organic acids!
Wow!
Back to my point about each county needing to explore its own biological zoo in virgin land before it is too late.

Utilization of Phosphate Solubilizing Microorganisms


Japan has only very small amounts of rock phosphate, and most of its soils immobilize phosphate ions into unavailable forms. Rock phosphate which can be mined by current technology is predicted to become exhausted in about 100 years' time.

Therefore, there is a strong interest in developing alternative sources of phosphate fertilizer. Many countries are studying the direct utilization of
rock phosphate. Australia has developed "biosuper", i.e. pellets composed of rock phosphate, sulfur and sulfur-oxidizing bacteria. Japanese scientists are very interested in the solubilization of bound phosphate in soil which has accumulated phosphate from repeated, heavy applications of phosphate fertilizer.

While more than 70% of total phosphate is present in organic forms, such as inositol phosphate in volcanic ash soils, there are very few
indigenous microorganisms with a strong ability to decompose inositol phosphate in the soil. On the contrary, Japanese soils contain many indigenous heterotrophic microorganisms which solubilize mineral bound
phosphates by the excretion of chelating organic acids.
In grassland soils, phosphate solubilizing microorganisms made up 1% of bacterial populations and 10% of fungal populations (Nishio 1985).
Tinker (1980) raised doubts on the utilization of heterorophic phosphate solubilizing microorganisms, because they need a large amount of organic matter before they can excrete organic acids.
Even if phosphate is solubilized, phosphate ions are incorporated into the
microbial biomass, so roots cannot absorb enough
of them.
Thus, we adopted the following strategy:
a) The addition of a large amount of organic matter makes phosphate solubilizing (PS) microorganisms proliferate and these solubilize bound phosphate.

b) Solubilized phosphates are incorporated into the microbial biomass during other microbial multiplication, using organic matter.

c) Once the organic matter becomes exhausted, the microbial
biomass decreases and releases phosphate into the soil.

d) The death of the microbial biomass can be accelerated by various soil treatments, including tillage, drying, liming and sterilization.

e) Plants can absorb phosphate after microbial proliferation has ceased.

f) The absorption of phosphate by plants can be accelerated by inoculation
with AMF.

Experimental Evidence

This is an interesting article, a link from the TP list home site
Microbial Fertilizers in Japan

I only just learnt this about Hypography

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