Hypography Science Forum Upgrades Terra Preta Discussion

The Hypography Science Forum has upgraded the terra preta discussion from a long, 43 page thread to a forum, with separate threads for charcoal making, gardening experiences, news, etc. The new location is here.

A recent message posted to the forum, from Janice Thies, Cornell University, is most interesting:

I am extremely heartened by the very positive response to the idea of using of biochar in agriculture and horticulture and appreciate your desires to put it to immediate beneficial use in these systems.

My name is Janice Thies. I am a soil microbial ecologist. I have been working with Johannes Lehmann at Cornell University for the past 6 years on various aspects of terra preta (microbial ecology in its natural state) and agrichar (how microbial populations respond to adding biochar to soil). It took us three years to convince the National Science Foundation that we were on to something here and to obtain funding for some of the basic research that is necessary for us to provide the data needed to answer your questions with confidence. Hence, we are several years behind where we could have been if funding had been available earlier. Even now, we continue to seek support for doing the types of tests many of you are most interested in. The results of our NSF funded research are just now being published or written up, but we are still a long way from being able to answer everything.

Currently, there are 10 research laboratories around the world that are testing char made from bamboo that was prepared at 5 different temperatures in the range we believe is likely to provide char that will be most beneficial for both plant production and C sequestration purposes. Rob Flannigan prepared the char in China and has engaged us all to do a wide range of testing on it. So, we should have some news about what temperature range might be best reasonably soon, but it is still early days.

Bio-char amended plots respond more favorably if adequate nitrogen fertilizer is provided. This is consistent with a previous observation here that added nitrogen is desirable when increasing soil microbial biomass.

One of the reasons that Dr. Lehmann recommends caution in the use of biochar can be seen in the paper recently published by Christoph Steiner et al., mentioned in previous messages. He did get excellent plant growth responses to adding biochar - as long as mineral fertilizer was also used. When you look at plant growth in the biochar only treatment, growth was worse than doing nothing at all (check plots). In the nutrient-poor and highly leached soils of the tropics, the added biochar likely bound whatever nutrients were present in the soil solution and these became unavailable for plant uptake. These results should make you cautious as well. How fertile a soil needs to be for biochar not to reduce plant growth or exactly how much fertilizer and/or compost should be added to be sure there is good, sustained release of nutrients, will likely vary soil to soil and we simply do not have these data available at present to make proper recommendations. So, keep this in mind as you do your own trials with your own soils or mixes. Try to follow good design practices for your trials, with replicates, so that you can judge for yourself what amount and type of biochar works best in combination with what amounts and types of fertilizers or composts you use (depending on the philosophy behind your cultural practices).

The soil microbial community in terra preta is different from that of surrounding soils, yet is repeatable over great distances. Actinomycetes bacteria seem to have a particular affinity for terra preta.

As to the 'wee beasties' or 'critters' as I like to call them, we have made progress on this front over the last several years. Brendan O'Neill and Julie Grossman in my laboratory, Sui Mai Tsai, our Brazilian collaborator at CENA and the University of Sao Paulo, and Biqing Liang, and many others in Johannes Lehmann's laboratory have been characterizing microbial populations in three different terra preta soils and comparing these to the adjacent, unmodified soils near by to them. Brendan found that populations of culturable bacteria and fungi are higher in the terra preta soils, as compared to the unmodified soils, in all cases. Yet, Biqing found that the respiratory activity of these populations is lower (see Liang et al., 2006), even when fresh organic matter is added. This alone means that the turnover of organic matter is slower in the terra preta soils - suggesting that the presence of black C in the terra pretas is helping to stabilize labile organic matter and is itself not turning over in the short term. All good news for C sequestration. However, since the respiratory activity is lower (slower decomposition), this may lead to slower release of other mineral nutrient associated with the fresh organic inputs. In some circumstances this is a good thing (maintaining nutrient release over the growing season), in other circumstances (more immobilization), perhaps not. We need more work on this to understand the implications of these results more fully.

Julie Grossman, Brendan O'Neill, Lauren McPhillips and Dr. Tsai have all been working on the molecular ecology of these soils along with me. So far, what we know is that both bacterial and fungal communities differ strongly between the terra pretas and the unmodified soils, but that the populations are similar between the terra preta soils. These results are both interesting and encouraging. First, that the terra preta soils (sampled from sites many kilometers apart) are more similar to each other than to their closest unmodified soil (sampled within 500 m) tells us that the conditions in the terra pretas encourage the colonization of these soils by similar groups of organisms that are adapted them. Our group has been working on cloning and sequencing both isolates from the terra preta soils and DNA extracted directly from them. A number of bacteria that were isolated only from the terra preta soils are related to the actinomycetes, but have not yet been described yet and are not very closely related to other sequences of known organisms in the public genetic databases. This is also very interesting. Some of you will know that actinomycetes have many unusual metabolic capabilities and can degrade a very wide range of substrates. Also, many are thermophilic and play important roles in the composting process. We have yet to fully characterize these organisms, but are optimistic that in time we can make some recommendations about what organisms or combinations of organisms might make a good inoculant for container-based biochar use. Two papers describing these results are in their final editing stages and will be submitted for publication in the journal 'Microbial Ecology' within the next few weeks. So, keep an eye out for them in several months time.

The prospect that glomalin might play an important role in terra preta needs to be approached with caution.

I want to add a word of caution about getting too excited about glomalin. Another of my students, Daniel Clune, has been working on this topic and his work suggests that the glycoprotein referred to as 'glomalin' in the literature - operationally defined as the protein extractable in a citrate buffer with repeated autoclaving - is not what it has been purported to be. First, the proteins extractable by this method are from a wide range of sources, not just arbuscular mycorrhizal fungi. Second, it has a shorter turnover time than has been suggested. Third, in a test with hundreds of samples taken from field trials varying in age from 7 to 12 to 34 years, its relationship with aggregate stability is suggestive at best. Dan's work is also being written up right now and should also be submitted for publication soon.

Could archaea be important?

Some field trials with bamboo char have been conducted in China, with very positive results. Look for upcoming papers from Dr. Zheng of the Bamboo Institute in Hangzhou. Another student in my laboratory, Hongyan Jin, is working with the soils from this experiment to characterize the abundance, activity and diversity of the soil bacteria and archaea. Her first results will be presented at the upcoming conference on Agrichar to be held in Terrigal, NSW, Australia, at the end of April/beginning of May this year. Please be sure to see her poster should you attend this conference.

Janice's recipe for char based potting soil:

Lastly, from my personal gardening experiences, I use spent charcoal from the filters of the 14 aquaria I maintain for my viewing pleasure. I combine it as about 5% of my mix with 65% peat moss, 10% vermicompost (from my worm bin in my basement where I compost all my household kitchen waste - aged and stabilized, not fresh!), 5-10% leaf mulch (composted on my leafy property in NY), 5-7% perlite to increase drainage, decrease bulk density and improve water retention and percolation, and some bone meal and blood meal (to taste :-) ). This makes an excellent potting mix for my indoor 'forest'. I am very much still playing around with this.

I hope this very long posting helps those of you feeling frustrated and wanting answers. Many labs are working on many fronts, but it is early days and we are trying to answer some fundamental questions first and then use the information to guide our field tests and recommendations.

I hope to meet some of you at the Agrichar Conference (see details at the conference website) http://www.iaiconference.org/images/IAI_brochure_5.pdf
The Cornell work and that of many of our colleagues in Brazil, China, the US, Australia and elsewhere will be presented, along with that of many others actively working on agrichar production and use around the world.

Good luck with your own testing and kind regards,

Janice Thies - jet25 at cornell.edu
719 Bradfield Hall, Ithaca, NY 14853

Technorati Tags: terra preta archaea bacteria soil microbiology bio-char garden glomalin

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. From Montana State University:

Some soil bacteria and fungi can access otherwise unavailable phosphorus, and some are commercially available. In a study on barley, one of these bacteria increased phosphorus availability by about 10 percent. In another study, a phosphate-solubilizing fungus was found to increase spring wheat grain yield by nine percent. "For both studies, the economics need to be considered to determine if these increases are worthwhile, and additional research is needed to determine the effectiveness of these products for different crops and soils," Jones said.

Growing your own biofertilizer may not be that difficult, depending on what it is you are trying to grow. Pictured is some compost tea starter I am "growing" for tomorrow's 36 hour run of actively aerated compost tea. I am going for a fungi-rich tea. Since the aerated tea process favors population growth of bacteria (and, one would think, archaea) over fungi, I am giving the fungi a boost before I start the tea. To 2 cups of compost, I have mixed in 3 tbs oat bran (the white flecks) and 1 tsp of T and J Enterprises (Spokane, WA)'s trichoderma rich "Soil Life & Activator" mix. As you can see the fungi is doing mighty fine. My first couple runs at promoting fungi growth were not as successful. By the looks of this one I am starting to get the hang of it.

Technorati Tags: fungi bacteria garden microbiology organic phosphorus soil

The Smell of Healthy Soil

Actinobacteria are a hyphae-producing soil bacteria that, in appearance and behavior, appear to have more in common with soil fungi. Like fungi, they decompose some of the more resistant forms of organic plant residues. Like fungi, they form branching filaments, which resemble the mycelia of fungi. Actinobacteria were originally classified as fungi under the older name Actinomycetes.

As bacteria, Actinobacteria have cell walls. They grow best in soil when conditions are damp and warm, playing an important role in decomposition of organic materials, such as cellulose and chitin. When the soil dries they produce spores. The wetness and force of rainfall kick these tiny spores up into the air. The moist air easily carries the spores to us so we breathe them in. These spores have a distinctive, earthy smell we often associate with rainfall. The smell comes from a compound, geosmin, which translates to "earth smell". The human nose is exquisitely sensitive to geosmin, able to detect it at concentrations down to 10 parts per trillion. Since the bacteria thrives in moist soil but releases the spores once the soil dries out, the smell is most acute after a rain that follows a dry spell, although you'll notice it to some degree after most rainstorms. Actinobacteria are important to healthy soil function, and are ubiquitous. Thus the smell of healthy soil is similar the world over.

Though they play an important role in soil quality, Actinobacteria are more commonly known for what it produces in the laboratory. Actinobacteria are unsurpassed in their ability to produce many compounds that have pharmaceutically useful properties. In 1940 Selman Waksman discovered that they made actinomycin, a discovery for which he was awarded a Nobel Prize. Hundreds of naturally occurring antibiotics have been discovered in these terrestrial microorganisms, especially from the genus Streptomyces.

Actinobacteria are also involved in nitrogen fixation; they convert atmospheric nitrogen into a form that can be used by plants.

Photo source: the earth smells good
Originally uploaded by kamalawalabear

Technorati Tags: soil bacteria smell

Teaming with Microbes Arrived Today

My anticipated copy of "Teaming with Microbes" has arrived. While I can't comment on the full text with any authority yet, I can say that it is well organized and has an extensive index (8 pages). It pleased me no end to see "soil science 28 - 42". There is also a valuable guide to labs and suppliers (4 pages). A supplier of mycorhhizal fungi here in Spokane is going to be getting a new customer.

My current soil obsession, bio-char, the foundational ingredient in terra preta nova, is disappointingly not mentioned. I have gotten the impression that Elaine Ingham, who has achieved demi-goddess standing in soil-web circles, was unswervingly skeptical of charcoal in large volumes as a soil amendment at the time the book went to publication, so I am not particularly surprised. In the post I saw, she based her concern on charcoal's high C:N ration putting soils out of balance. I'm chalking this up to fear of the unfamiliar. Too bad. Elaine Ingham is highly influential. When she comes around, her endorsement will save lives.

My restaurateur grandfather had a personal test to see if a chef was up to his standards: if the butter dish arrived without ice, he lowered his expectation that anything else could be properly prepared. I make similar menu-wide judgements on my orders of eggs-over-easy and chile rellenos. My acid test for an elightened organic gardening book is the treatment of glomalin (recalcitrant mycorhhizal fungally produced glycoprotein that accounts for 1/3 of world soil carbon). It is mentioned on page 37 (see familiar glomalin photo on page 39), so things are looking up at this point.

Tech Tags: bacteria book review environment fertility fungi garden glomalin microbiology new organic science soil

MPOG - Microbial Prospection for Oil and Gas

Microbial Prospectation looks for anomolies in microbial populations. The presence of various groups of methane-, propane- and butane-oxidizing micro-organisms can reliably differentiate between prospective and non-prospective areas, as well as between oil and gas reservoirs. The result of many years of exerience, the success rate exceeds 90%. This stand-alone approach is inexpensive, probably benefiting from recent computational improvements in characterizing microbial genetic characteristics. Makes you wonder what other benefits will accrue from these types of advances.

Read more at Microbial Prospection and Recovery for Oil and Gas

Tip from: OilNetCom Blog

Tech Tags: soil microbiology science

Orange ooze gives clues for those in the know.

If you walk your property with an eye to understanding how it works, knowing what orange ooze is and what it means is a worthy skill. Orange ooze forms where anaerobic waters seep from the ground. This can be a good and natural thing, as in the image.
Reduced iron (Fe(II)) is a source of energy for life, including iron-oxidizing bacteria. The oxidized iron gives orange ooze its distinctive color. Another distinctive feature of anaerobic waters is a surface sheen, reminiscent in appearance of an oil sheen, but brittle.
Anaerobic waters form for specific reasons.
Unfortunately, one reason is contamination. A classic source of Fe(II) laden waters are acidified drain waters associated with mining and industrial wastes. Other reasons are septic systems, waste water lagoons and land fill leachate. Fuel leaking from a transfer line is a classic source. Any substance that can be rapidly decomposed by microbial activity, even a benign dust control product like lignin sulfonate, can result in anaerobic groundwater if concentrated by runoff in a roadside ditch.
Anaerobic groundwater formation is usually natural. Examples are flows through wetland conditions (as in the image) and through pond bottoms. In natural cases, orange ooze relates to elevated microbial activity. This biological activity usually needs a temperature above 41 degrees F (5 decrees C) and an adequate food supply to support microbial respiration in excess of oxygen supplies.
Now look closely at the image. Notice the greenest vegetation is in the band of water with the anaerobic sheen, parallel, and below the orange ooze. That is because the seep water is warmer than the surface water it is flowing into, stimulating a difference in plant growth. The elevation of the orange ooze shows the anaerobic water is dropping into the stream. Not shown is that it is on only one side of the stream and only along a limited stretch. This gives important clues as to where to look for the source, in this case wetland conditions in the pasture adjoining the stream. The warmth of the seep indicates that the hydrology supporting wetland living conditions is not localized winter precipitation and snow melt, but has deeper, less seasonal, origins.

Tech Tags: Soil science tips microbiology environment metal health wetland

New organic garden book: Teaming With Microbes

For over 30 years, Jeff Lowenfels has written a free-lance gardening column in Anchorage. Among other things, Lowenfels and a couple of like-minded friends have patented a cool one-eye device for looking at plants and insects in the field, the macroscope, available now through Brunton. Lowenfels now has a forthcoming book on soil microbes, a subject he has written and lectured on abundantly for the last 5 years. He has been promising a book on this for most of those years and a lot of gardeners are looking forward to it. The subject of microbes and plant nutrition offers a lot to get excited about. I've mentioned some bits a time or two. And, as back40 reminds us, it was only in 1996 that glomalin was discovered. Glomalin is the durable soil carbon produced by mycorrhizal fungi and responsible for many positive attributes of soil function, plant nutrition and soil health.
According to a news article this week, Lowenfels book "Teaming With Microbes: A Gardener's Guide to Using the Soil Food Web." is being published by Timber Press and is due out sometime in late summer. Tag me "easily entertained", but I really like the double sens of the word "teaming" in the book title. In 2004, the working title was "Soil Science for Gardeners", and thankfully Lowenfels has wisely prevailed upon Timber Press to use "Teaming With Microbes" as he originally proposed.

Tech Tags: soil science research health fertilizer nutrition microbiology fungus glomalin bacteria nematodes new organic garden book microbes

Tap Roots

Some plant species do the opposite of saving for a rainy day. They sop up rain water that would otherwise run off or evaporate. They redistribute the water to a long tap root where it is safely stored in deep soil out of reach of their shallower rooted neighbors. In the intervals between rainy periods, they return water to the shallow portion of the root system and prevent it from drying out. Researchers indicate that this capability is not restricted to the tree species in the the Amazon basin they researched. While the researchers refer to the "hydraulic redistribution" phenomenon being observed by others, first in small plants two decades ago, this appears to be the first time that a statement has been offered to gage the potential global scale and the significance to water balance and climate models.

The new study in the Amazonian forest shows that trees use water in a complex way: The tap roots transfer rainwater from the surface to reservoirs deep underground and redistribute water upwards after the rains to keep the top layers moist, ... The researchers estimate this effect increases photosynthesis and the evaporation of water from plants, called transpiration, by 40 percent in the dry season, when photosynthesis otherwise would be limited.

"This shifting of water by roots has a physiological effect on the plants, letting them pull more carbon dioxide from the atmosphere as they conduct more photosynthesis," said co-author Todd Dawson, professor of integrative biology at UC Berkeley. "Because this has not been considered until now, people have likely underestimated the amount of carbon taken up by the Amazon and underestimated the impact of Amazonian deforestation on climate."...

Dawson, Lee and their colleagues, including Inez Fung of UC Berkeley, reported their findings last month in the Dec. 6 issue of the Proceedings of the National Academy of Sciences. ...

"Evapotranspiration stays higher than previously expected during the prolonged dry season because of this private reserve of water banked during the wet season by the tap roots," said Dawson. "Just as perspiration cools us off, increased transpiration by trees in June and July explains the drop in temperature in the Amazon."

This effect changes the way the atmosphere heats and cools, and will change the way rain is distributed, he noted. Depending on the extent to which trees elsewhere in the world, especially in Africa and other tropical and extratropical areas, redistribute water in the soil, the impact on global climate could be significant.

"The impact on transpiration is greatest in the Amazon and Congo forests, but our model also shows an impact in the United States and other places that have dry and wet periods," Lee said.

Trees have long been known to lift water from the soil to great heights using a principle called hydraulic lift, with energy supplied by evaporation of water from leaf openings called stomata. Twenty years ago, however, some small plants were found to do more than lift water from the soil to the leaves - they also lifted deep water with their tap root and deposited it in shallow soil for use at a later time, and reversed the process during the rainy season to push water into storage deep underground. Dawson discovered in 1990 that trees do this, too, and to date, so-called hydraulic redistribution has been found in some 60 separate deeply rooted plant species.

Earlier this year, Dawson's colleague and former UC Berkeley doctoral student Rafael Oliveira of the Laboratório de Ecologia Isotópica at the University of Sao Paulo, Brazil, discovered that Amazonian trees also use hydraulic redistribution to maintain the moisture around their shallow roots during the long dry season. During the wet season, these plants can store as much as 10 percent of the annual precipitation as deep as 13 meters (43 feet) underground, to be tapped during the dry months. [emphasis added]

"These trees are using their root system to redistribute water into different soil compartments," Dawson said. "This allows the trees and the forest to sustain water use throughout the dry season."

The process is a passive one, he noted, driven by chemical potential gradients, with tree roots acting like pipes to allow water to shift around much faster than it could otherwise percolate through the soil. In many plants that exhibit hydraulic redistribution, the tap roots are like the part of an iceberg below water. In some cases these roots can reach down more than 100 times the height of the plant above ground. Such deep roots make sense if their purpose is to redistribute water during the dry season for use by the plant's shallow roots, though Dawson suspects that the real reason for keeping the surface soil moist is to make it easier for the plant to take in nutrients.

"Hydraulic redistribution is definitely related to water, but it can't really be discussed outside the context of plant nutrition," he said.

The article goes on from there, but this point concerning nutrition is worth expanding upon. The article indicates that stored water is transferred to the shallower portion of the root system where it must exude into the soil "for keeping the surface soil moist". Soil ion adsorption and plant nutrient exchange processes are moist (vs dry) soil phenomena. Keeping the soil moist just at the root surface would put minimal demand on plant water reserves but have a significant effect on nutrient availability.

It would also support the symbiotic community of soil microorganisms supported by the root system. Arbuscular mycorrhizal fungi and symbiotic soil bacteria are sustained by rhizodeposition, a term which can encompass both liquid root exudates and solid plant cell material. In my experience, root exudates are normally explained as simply an energy or carbon source for the microbes, a carbohydrate quid-pro-quo in exchange for mineral nutrients. It is a fairly thrifty exchange. The water supply component of root exudates highlighted in this new research is an exciting emphasis, at least to your author. Access to steady and stable supply of water, even a parsimonious supply, is ideal for sustaining soil fungi. Resulting beneficial effects, in the form of mycorrhizal hyphae, can extend out from a few centimeters to many meters. Perhaps future observations will be able to determine if the fungi component also plays a role in moistening soil.

Root water uptake and the dynamic availability of water to plants is a phenomenon that tends to be overlooked by soil scientists, despite the often dominant role of roots as a sink for water in the soil.

quoted from: Roots: The big movers of water and chemical in soil. Clothier, BE; Green, SR. Soil Science. Vol. 162, no. 8, pp. 534-543. Aug 1997.

Color photo is from http://earthobservatory.nasa.gov/Laboratory/ICE/Images/panama_canopy.jpg

Line drawing to left is Fig.113.--Root of sunflower where plants were spaced 8 inches apart. From Root Development of Field Crops. Weaver, John. 1926 posted at http://www.soilandhealth.org/

Line drawing in middle of article is from
How a Tree Grows, FS-32, 1970, USDA Forest Service
Key:
(A) Tap Root — Provides main support of tree and anchors it firmly in the ground. (Not all trees have one)
(B) Lateral Roots — Help support and anchor trunk, may extend far out, beyond crown spread.
(C) Fibrous Roots — Masses of fine feeding roots close to ground surface.
(D) Deeply Descending Roots (‘Sinkers’) — Grow downward from lateral roots

EurekaAlert! news release for cited article
UPI news release for cited article

Technorati Tags: Soil science Environment Water Soil Microbiology Science

Diversity

The current round of research into soil microbial life holds the door open onto insights that stagger the imagination.
Discoveries about vesicular arbuscular mycorrhizal fungi (VAM) and arbuscular mycorrhizal fungi (AMF) transformed our understanding of the contribution of soil fungi to soil function. Current research indicates that similarly monumental discoveries may await us.

Genome research and computational improvements demonstrate that the number and diversity of soil bacteria species far exceed the levels anticipated.

Bacteria make up the bulk of life on Earth and play a vital role in the lives of other organisms. But scientists have barely scraped the surface when it comes to identifying bacteria – 99% of species cannot be grown by standard techniques in the laboratory. ... Soil is ... a complex microbial environment containing thousands of distinct species – most of them bacteria – in just a half-gram sample.

and

More than one million distinct genomes occurred in the pristine soil, exceeding previous estimates by two orders of magnitude.

The distribution of this diversity is unequal in ways that may seem counter intuitive. The following was reported earlier today in What's New in Science and Technology .

Ironically, in the diversity of soil bacteria, the otherwise species-rich Amazon is a more like a desert, while the arid desert is a teeming microbial Amazon, researchers have found. Their first-ever continental-scale genetic survey of soil bacteria revealed that the primary factor that seems to govern the diversity of soil bacteria is soil pH. Thus, the acidic soils of topical forests harbor fewer bacterial species than the neutral soils of deserts.

The researchers said that, since soil bacteria play a fundamental role in a vast array of ecological processes, their survey constitutes an initial step in a new research pathway to understanding that role.

As exciting as these studies are, they are tentative and simplistic in comparison to the dynamic they reveal. These results are the product of capacity building needed before the real work can begin.

Technorati Tags: Soil science Microbiology Research