transect points

I've posted on my concern for triclosan-containing products before. I think far too much of it is being land applied in our biosolids:

It makes little sense to land apply recalcitrant compounds that needlessly get rid of soil microbes. Fomenting the growth of resistant strains of disease organisms is only one concern. Soil functional capacity is largely mediated by living processes. It is the height of folly to jeopardize those functions for a useless consumer item.

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.

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).

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.

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.

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.

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

Soil data is "noisy" data. Being a difficult medium to observe and measure, soil has an almost weird capacity to mask change.

In several instances that I can recall, it seemed improvement in soil carbon status was not evident until several years after a change in management was made. The increases in soil organic matter called intervening data into question.

You can see similar data fluctuations due to individual samplers, but this delayed stepping pattern of carbon increase happens a little too often to ignore. It is as if the momentum for an increase in carbon must first collect in the biological dynamic of the soil, invisible to our simple agricultural analysis tools where we measure TKN, TOC and C:N ratios. Those were my thoughts as I read the following:

The Four Phases of No-Till

Phase one, initialization, occurs in the first five years. It is where soil structure starts to improve and microbial activity increases. Additional nitrogen is required to do that.

"As organic matter increases, you need the added nitrogen to make more of it," Towery said.

The second phase is transition from the fifth to tenth years. This is when organic matter accumulates, soil aggregation and soil microbial activity elevates, phosphorous accumulates, and nitrogen immobilization and greater mineralization occurs.

Phase three is consolidation, from 11 to 20 years. In this period, carbon accumulates and additional water is available in the soil. Further nitrogen mineralization and immobilization occurs and there is an increase in cation exchange capacity (CEC) and nutrient cycling.

"These years aren't perhaps exact, because this phase depends on your latitude and your soils," Towery said.

The fourth and final phase is maintenance, which comes after 20 years. It brings a continuous flow of nitrogen and carbon, greater availability of water and high nutrient cycling with increases in nitrogen and phosphorus.

"Twenty years is a long time. It's not like you've arrived at the Promised Land but things do change with the soil," Towery said. "It's because it is a dynamic system. The technology and management strategies you use changes over time as you go from phase to phase.

"One change we underestimate is the changes in soil biology. We can't see them but they're there."

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.

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.

The Godfather of Terra Preta, soil scientist Wim Sombroek (1934 - 2003) enjoyed a lifelong fascination with enhanced soil. The importance of plaggen soil in his native Netherlands impressed him at an early age, and early in the 1960's, he recognized in the Amazonian Dark Earths something familiar and precious. Before his passing, he assembled specific soil scientists, challenging them to discover the process for making and sustaining a modern equivalent of the bio-char enhanced terra preta, what he termed terra preta nova.

A great opportunity in answering Sombroek's challenge lies is surmounting the opacity of mutualistic rhizospheric species to traditional analytical approaches: only 1% of rhizospheric species are cultureable ala petri dish. We don't have a robust body of culture-independent studies against which to compare Terra Preta, so we are doubly challenged to reverse-engineer the phenomenon.

Considering Wim Somboek's many noteworthy accomplishments, the perspective of his international leadership, and the late-in-life timing of his challenge, one senses he is pointing us to a mystery fundamental to understanding soil in new and exciting ways. This happens at a time when the soil science profession is in dynamic transition and sorely in need of a unifying vision. Wim Sombroek has given soil scientists a most welcome and worthy quest.

Its in the news. Research shows that invasive earthworms are damaging forest soils and are a menace to species diversity. Brought to light in November, 2002, gardening experts have confirmed the concern and the news keeps spreading. Fortunate for inquiring minds, self-archived copies of published journal articles are available. The problem is most often associated with formerly glaciated regions, where native populations of earthworms are not present. One work has a general map of affected locations (can compare to map here).

Another work addresses damage to soil. Comparing soil in front of the invaders to post invasion conditions demonstrates that these worms cause soil compaction, reduce soil fertility, increase erosion. Alterations in the soil profile include thickening of A horizons and obliteration of E horizons. I am still processing this information, but it appears that these invaders are capable of alterations deep enough into the soil profile to result in a change in soil taxonomic classification at the order level.

What looks to be one of the more prominent invasive species, Lumbricus rubellus showed up in my maple leaf compost (now vermicompost). I can confirm that L. rubellus is voracious. I remember a shovel slice of some nearby soil that went in a week or so before L. rubellus showed so my guess is they came with the place. L. rubellus operates on the surface litter and organic material found where that layer rests on the mineral soil. There are strong indications that L. rubellus supplements its leafy diet by feeding on the fungi and bacteria in the rhizosphere of plant roots. Seeing first hand how these critters operate, I find this last aspect quite disturbing. With its carbon sequestration function and the highly mutualistic species that it supports, this planet needs all the rhizospheric biological capacity it can muster.

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

This UPI article is inspiring. Appreciate the dedication of the subject and the Bill and Melinda Gates Foundation for supporting this work.

Peter Hotez has spearheaded a 25-year fight to eradicate hookworm, and 12 other neglected diseases, illnesses of the poor and powerless. These ailments bear frightening names such as leishmaniasis, human African trypanosomiasis and schistosomiasis. Some are vector-borne diseases, spread through animals or mosquitoes, others are bacterial, and many more are caused by worm infections.
"When you work on a neglected disease, you're neglected by your scientific colleagues. It's hard to be taken seriously sometimes," Hotez says.
"He's the ideal scientist -- someone who is honest, works hard, and is passionate about what he is doing," says H.R. Shepherd, the chairman of the Sabin Institute who has known Peter for almost 10 years.
Hotez is developing the world's first hookworm vaccine, now in Phase 1 trials, and he'll know for sure if it works by 2011.

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.

Atmospheric CO₂ concentration is expected to increase by 50% near the middle of this century. Indications are strong that rising CO₂ effects higher soil organic carbon content in some cases. Glomalin, which accounts for 1/3 of soil carbon, is of particular interest because of its important role in binding soil aggregates and increasing nitrogen use efficiency. The Center for the Study of Carbon Dioxide and Global Change has updated their excellent summary about the CO₂ - glomalin relationship. There is a great reference list to dive into.