Long-Term Soil Ecosystem Studies

Hello folks,

The current issue of Nature has an editorial (appended below) that made me think of the archived samples at Rothamsted. I am not too concerned about Rothamsted sending its 200,000+ bottles to the landfill (or giving them as "amusing gifts to visiting scientists") but surely there are soil archives that have gotten too unwieldy and are at risk.... or that have already been jettisoned.

Perhaps we can make sure that Nature's new monthly series pays homage to an at-risk archive of soil samples (or other materials) from a long-term experiment...

Any thoughts ?

Joel

*******************************************************************8
Editorial

Nature 451, 500 (31 January 2008) | doi:10.1038/451500a;
Published online 30 January 2008

Secret treasure-troves restored

Reflecting on the endeavours of scientists past can provide both inspiration and pleasure.

The face of science is always turned to the future — and that has been the downfall of many a historic scientific collection outside of the
mainstream museums.

Take the eighteenth- and nineteenth-century natural-history collection begun in the 1770s by Lazzaro Spallanzani at the University of Pavia in northern Italy. In the 1930s, the half-million stuffed specimens — from giant turtles to gibbons — were cleared out to make room for a new faculty of law. The collection had become a slight embarrassment, a woefully old-fashioned way of doing science. After sojourning at a nearby palazzo, it was carelessly crammed into the attics of the local Visconti castle for storage. But even the finest address can host insects and microbes, and over the years the collection began to rot.

Similar fates befell other collections around Europe. At best, individual items would be given as amusing gifts to visiting scientists, at worst, the whole lot would be thrown away. Research interests had moved on, teaching methods modernized and, when the student numbers mushroomed after the 1960s, space was needed by new faculty members.

But in recent years a fresh awareness has developed about such relics,stirring first in Italy, whose scientific history, from the Renaissance to the start of the twentieth century, is arguably the most important on the continent. In 1991, the Italian association of university rectors set up a committee specifically to ensure that collections in universities were catalogued and cared for. In 2004, the Italian government was persuaded to amend its law on cultural heritage
to include the protection of scientific objects, and the next year the Council of Europe passed a like-minded resolution addressing universities across the continent.

In recent years a fresh awareness has developed about historic scientific collections.

Germany was alerted to what is hidden in the forgotten corners of its old universities when those in eastern Germany were required to make inventories at the time of reunification. A project to comprehensively digitize the collections in all the nation's universities is now under way.

Even so, there is little money across the continent for restoration. Back in Pavia, the university cannot find the resources to speed up the painstaking rescue of some of Spallanzani's specimens, and many will be lost forever. On the other hand, several of its other collections have survived well — and they form the basis of the first in Nature's new monthly series paying homage to relatively unknown collections and other scientific monuments off the well-beaten museum track (see page 526 ). The series will, we hope, inspire a greater interest in where
scientists have come from, as well as encouraging those on the conference circuit with a few hours to spare to visit them. Delight is guaranteed.

Recently Arlene Tugel and Garrett Liles (student at Davis) mentioned interest in sample archiving. This should be (if it isn't already) on our list of potential new projects/papers for our network. This is an absolutely great topic that could be explored much more than is in the literature currently. Extremely important.

Dr. Poulton at Rothamsted has some information on Rothamsted practice and I will get permission to post and share these!!

Dan Richter

Not only long term experiments themselves are a rich source of information, archived soil samples can yield valuable information too. Reanalyzing archived samples for historical trends in e.g. PCB levels is an accepted approach (e.g.: Alcock, R.E. et al. 1993. Environmental Science and Technology 27: 1918-1923). We recently used PCR-DGGE on historical soil samples from long-term field experiments and observed systematic differences between samples from soils that had received different treatments. Hence we wrote a letter to editor of Science, which was published in slightly modified form in Science (2004), 306, 813.

The original letter is presented below:

Bacterial Diversity in Archived Agricultural Soils

J. Dolfing, A. Vos, J. Bloem, P.A.I. Ehlert, N.B. Naumova, P.J. Kuikman

Bacterial diversity and bacterially mediated processes are considered key to soil ecosystem functioning with processes such as decomposition and mineralization (1). However, our understanding how the activity and diversity of prokaryotic communities responds to changes in the environment is limited (2). At present, gradual changes in biodiversity have to be assessed by real time monitoring of long-term field experiments. Such experimentation is costly and requires long-term commitment of researchers and funding. We explored a more rapid approach and used PCR-DGGE to show that existing soil archives with material from documented long-term field trials in the past can be useful in identifying effects of environmental parameters on microbial diversity (3).

Alterra, as a number of other research institutes, has a soils archive with, in our case, samples that are up to 120 years old. In a first screening we selected a series of samples from the 1950s to 1970s from an experiment that was initiated in 1940 (4). The field with a sandy soil in the eastern part of the Netherlands had been farmed with a crop rotation of potatoes, rye and oats. We selected samples from years with rye as crop. Time series from two field plots were analyzed, one from a plot that had received animal manure and another from a plot that had received chemical fertilizer. Genetic diversity in the archived soil samples was analyzed with 16S-based denaturing gradient gel electrophoresis (PCR-DGGE) of total soil extracted DNA (5). From densitometric profiling and multivariate analysis of the gels (6) it is clear that the community structure of manure amended soils clearly differs from the community structure of the soil that had received no manure and only mineral fertilizer. From this and other results (7) we conclude that it is possible to detect systematic differences in soil microbial community composition in samples that have been dried and stored for more than 50 years.

Soil microbial biodiversity is presently getting major attention from both researchers and policy makers (EU Soil Strategy, International Biodiversity Agreements, OECD expert meetings). The present results are a first step towards unlocking biodiversity information present in archived soil samples. More specific methods (including sequencing of PCR amplified DNA) will undoubtedly provide more specific information on the type of organisms present in archived samples. Analyses of archived soil samples can provide a reference condition for soil biodiversity that has no or little interference from intensive human activities, and give clues on sustainable use of agricultural soils. Furthermore they will provide a database for answering questions on effects of management decisions (e.g. fertilization), land use and climate change, and atmospheric deposition on soil microbial diversity. A parallel with environmental and geochemical studies on sediment and ice cores comes to mind. As culture collections are limited to organisms per se, the important and promising feature of archived soil samples is that they contain information on community composition.

1. P. Nannipieri et al., Eur. J. Soil Science 54, 655 (2003).
2. D. H. Buckley, T. M. Schmidt, Environ. Microbiol. 5, 441 (2003)
3. G. A. Kowalchuk, F. J. de Bruijn, I. M. Head, A. D. L. Akkermans, J. D. van Elsas, Molecular Microbial Ecology Manual (Kluwer Academic Publishers, Dordrecht, ed. 2, 2004).
4. J. Kortleven “Kwantitatieve aspecten van humusopbouw en humusafbraak” (Verslagen van landbouwkundige onderzoekingen nr 69.1., Pudoc, Wageningen, 1963).
5. G. Muyzer, E. C. de Waal, A. G. Uitterlinden, Appl. Environ. Microbiol. 59,695 (1993).
6. O. Dilly, J. Bloem, A. Vos, J. C. Munch, Appl. Environ. Microbiol. 70, 468 (2004).
7. J. Dolfing, A. Vos, J. Bloem, P.J. Kuikman, data not shown.

so far the letter.

More details on our endeavours to use archived soil samples for microbiological research are presented in short report:

J. Dolfing, A. Vos, J. Bloem, P.J. Kuikman. 2004. Microbial diversity in archived agricultural soils. Alterra report 916, Alterra, Wageningen, the Netherlands.

The report can be downloaded from:

www.alterra.wur.nl/Internet/Modules/pub/PDFFiles/Alterrarapporten/Alterr...

Another publication where archived soils samples were re-analyzed with modern molecular tools is:

Tzeneva VA, Li YG, Felske ADM, de Vos WM, Akkermans ADL, Vaughan EE & Smidt H. 2004. Development and application of a selective PCR-denaturing gradient gel electrophoresis approach to detect a recently cultivated Bacillus group predominant in soil.
Applied and Environmental Microbiology 70: 5801-5809 (2004).

We conclude that archived soils are a promising repository of biological information. More research is still needed, especially on the effects of milling and drying on the soil microbiota.