Soil Science Journal Club : reading

Next journal club meeting - carbon in China

Andrew.Rate — Wed, 01 Jul 2009 05:41:00 GMT

The next meeting (already notified by Talitha) is on Tuesday 7 July, 1pm, second-floor lunch area, Soil Science building, UWA.

The article to be mused upon is :
Piao S, Fang J, Ciais P, Peylin P, Huang Y, Sitch S, Wang T. 2009. Carbon balance of terrestrial ecosystems in China. Nature, 458:1009-1014.

Small data set, high impact

Andrew.Rate — Thu, 11 Jun 2009 01:52:00 GMT

[Musings by Talitha Santini]

The first article for the revived Journal Club was ‘Jarosite as an indicator of water-limited chemical weathering on Mars' (Elwood Madden et al. [2004] Nature, 431:821-823), chosen by Talitha because it was a short and reasonably simple article about soils on another planet. The authors used observations of jarosite and gypsum as alteration products of the basaltic parent rock at the Meridiani Planum landing site on Mars to argue a case for chemical weathering on Mars being water-limited. Using geochemical modelling software, a basaltic mineral assemblage (using data from Rosenbauer et al. [1983]) was titrated into a fluid containing SO₄^2-, Na⁺, K⁺, Ca²⁺, Fe²⁺, Mg²⁺, Al³⁺, and dissolved SiO₂, under current Martian atmospheric O₂ and CO₂ fugacities, at 298 K and 10⁴Pa total atmospheric pressure. The authors modelled both mineral assemblages as basalt weathering progressed, and the final mineral assemblages at different water:rock ratios. Modelling indicated that jarosite could only be present as a result of basalt weathering if (a) a large quantity of water reacted completely with a small amount of rock (for example, water creating an alteration rind on rock surfaces); or (b) a small amount of water reacted only partially with a large amount of rock. It was concluded that once jarosite formed, water must have been removed quickly in order to halt chemical weathering before pH increased and jarosite was converted to an iron (oxy)hydroxide - hence the article's title.

Once we started examining the article, we realized how little data were required to have an article published in Nature. The authors used only five pieces of information about Mars (the presence of a basaltic parent rock, the presence of jarosite and gypsum, and Martian atmospheric O₂ and CO₂ fugacities and atmospheric pressure) and a geochemical model designed for Earth surface conditions. This got us thinking about having a look at some Martian soil data from NASA (presented in Rieder et al. [1997]) and publishing our own articles. It's a good example of researchers considering data critically and extracting as much information as possible with the tools they have available to them. The tools we have available aren't perfect though, and one of the criticisms of this article was the ‘Earth-centric' modelling - that is, the use of Earth surface conditions to simulate Martian weathering processes. Where possible, the authors used (current) Martian conditions; however, in the case of temperature and pressure, current Earth conditions were used.

The ‘suppression of mineral phases...at the discretion of the operator' also raised debate about using geochemical models to simulate weathering. The problem is that models generally predict phase assemblages at thermodynamic equilibrium, which may not actually occur in the field. The authors cite the example of slow goethite formation hindering its occurrence in acid mine drainage environments despite being the thermodynamically stable iron phase. Kinetics were only included in this model ‘through the suppression of mineral phases unlikely to form in a geologically relevant time period.'

So why should we care about soils on Mars, anyway? We came up with a few answers to this: for the pure basic science objectives of understanding the properties and history of Martian surface materials and understanding how soils develop under different environmental conditions; because soil on another planet is inherently interesting; and because we may even want to annex Mars one day as a replacement Earth, in which case an understanding of its soils would be pretty important.

The next article will be chosen by Bree, with the next meeting scheduled for July 1.

Image from www.andersonfreepress.net

I feel good, I feel stupid

Andrew.Rate — Thu, 28 May 2009 21:59:00 GMT

This was something I sent around to our School's postgraduate students, after being sent the article by Prof. Martin Fey:

Schwartz, M.A. (2008) The importance of stupidity in scientific research. Journal of Cell Science121:1771 .

This should be essential reading for postgraduate students in any discipline. (It's irrelevant that it's in a biology journal.) Essentially Schwartz's argument is that since research is on the very edge of human knowledge, feeling lost or stupid should be felt regularly by researchers. This normalisation of the self-doubt that many of us feel (and not just while doing our graduate research!) is surprisingly encouraging.

"...we don’t do a good enough job of teaching our students
how to be productively stupid – that is, if we don’t feel stupid it
means we’re not really trying."

It's great to see articles in scientific journals that acknowledge the humanity of researchers.

Image from www.cartoonstock.com

Journal club revived

Andrew.Rate — Mon, 18 May 2009 03:05:00 GMT

[Edit at 29 May 2009 - the date has been shifted to Wednesday 3 June]

The poster at right was prepared by Talitha to publicise the first meeting of the Soil Science Journal Club for 2009...

...we'll be discussing the article: Madden MEE, Bodnar RJ, Rimstidt JD. 2004. Jarosite as an indicator of water-limited chemical weathering on Mars. Nature, 431:821-823.

Maybe we'll see you there?

[The second-floor lunch area is on the top floor of the School of Earth & Environment (South) building (i.e. the Soil Science building).]

Digging for gold

Andrew.Rate — Thu, 06 Nov 2008 05:36:00 GMT

Musings on:
Anand RR, Cornelius M, Phang C, 2007. Use of vegetation and soil in mineral exploration in areas of transported overburden, Yilgarn Craton, Western Australia: a contribution towards understanding metal transportation processes.Geochemistry-Exploration Environment Analysis, 7: 267-288.

The use of soils and vegetation as sample media for geochemical exploration is not new. In recent years there seems to have been a resurgence of interest in sampling soils, and particularly plants, with the expectation that these media carry a signature of underlying ore bodies. In many cases the rock or regolith which hosts the ore body may be masked by transported sediments, so that even the weathered ghostly imprint of an ore may lie well below the surface.

Several mechanisms may allow the formation of signatures of ore bodies in surface soils, even in a transported overburden. In addition to purely chemical or physical processes, it is possible that plants can access ore-forming elements at depth, as deep roots search the regolith for water. Not only can this give anomalous concentrations of trace elements in plant tissues, but biological re-cycling can subsequently enrich surface soils with a signature of what lies beneath.

These ideas are the basis for Anand et al's. article. They took vegetation (mulga; Acacia aneura and related species) and soil samples across known but unexploited gold and/or base-metal (Cu, Zn, Ag) deposits in Western Australia, where much of the bedrock is covered by deeply weathered regolith profiles and, in many cases, transported sediments as well. They found that analysis of soils did not clearly delineate the vertical projection of underlying ores (even using selective extractions for trace elements which commonly improve signal:noise ratios). In contrast the living plant tissues, and particularly the litter layer, showed clear signatures of underlying mineralization, with peak concentrations in both media vertically over the ore body.

These results are of obviously practical importance to exploration geochemists, demonstrating that (at least in some instances) vegetation sampling and analysis offers an additional tool to "see through" weathered and/or transported material to ore bodies beneath. It is possibly more generally significant, from an "understanding the Earth" point of view, that vegetation may be important in redistributing trace elements in earth surface environments, particularly in arid regions where plants' search for water requires root growth to great depth. In such environments, geochemical signatures in soils may well be the result of millennia of plant uptake.

Image of the Moolart Well prospect from www.regisresources.com

New Comment on A Soil Scientist's Lament

Andrew.Rate — Fri, 24 Oct 2008 07:19:00 GMT

A new Comment has been posted in reply to A soil scientist's lament, by Professor Philippe Baveye (the author of the article mused upon in the original post).

It's well worth reading. You can get to it by clicking here, too (scroll down to the bottom of the page).

the soil on Mars

Andrew.Rate — Tue, 02 Sep 2008 03:15:00 GMT

...musings on Amundson R, Ewing S, Dietrich W, Sutter B, Owen J, Chadwick OA, Nishiizumi K, Walvoord M, McKay C. 2008. On the in situ aqueous alteration of soils on Mars. Geochimica et Cosmochimica Acta 72:3845-3864.

It's great when an article related to one's own discipline is about something exotic, and it would be hard to imagine a more exotic environment than the surface of Mars. I enjoy highlighting interesting developments to students, so this year's Introduction to Geochemistry students had the data from this article as an example when we learned about mass balance during weathering. And this was my first crack at teaching this geochemical topic to students as well, so I learned a lot too. We used the subject matter, if not the Martian data, in a prac class, using an excellent dataset published by Oh & Richter (2005).

Amundson et al.'s hypothesis is that liquid water must have existed on Mars at some stage in that planet's history, based on the mineralogical record (minerals which need water to form, such as smectites and jarosite, have been identified on the Martian surface). Amundson et al. further tested this hypothesis by using elemental analysis data from conveniently exposed "soil profiles" on Mars, within the Gusev and Endurance craters investigated by the Mars Exploration Rover (Opportunity) mission. They were looking for evidence of absolute loss or gain of elements which might reflect transport by liquid water - and they found exactly that. Soils were depleted in major rock-forming elements (Si, Al, Mg, Ca, Fe, etc.) relative to the likely parent materials (Gusev basalt, or aeolian dust), probably representing earlier weathering mediated by water. A key result was the enrichment in the soil profiles of sulfur, chlorine and bromine, consistent with the aqueous transport of sulfate, chloride and bromide salts followed by drying.

The point is also made that comparable environments (very dry and cold; e.g., some of Antarctica) exist on Earth, and similar soil-forming processes have occurred here (on Earth, that is!) as well. The authors refer to such terrestrial soils as being "abiotic"; a bit of a misnomer, I thought, where perhaps they meant the absence of higher organisms (surely some microorganisms were present in all the Earth examples - were they there on Mars?). Plus there is the usual issue with mass-balance approaches (fully acknowledged) of matching the weathered/altered material to its assumed parent material.

This was a fun article to read. It's not often that I get to read and use a publication that contains so much language usually reserved (in my reading experience) for science fiction - Mars landers, differences in gravity - all wonderful stuff.

Image from www.nasa.gov

News - Double-blind article reviews help female authors

Andrew.Rate — Tue, 17 Jun 2008 03:32:00 GMT

How's this for an eye-opener?

Budden AE, Tregenza T, Aarssen LW, Koricheva J, Leimu R, Lortie CJ. 2008. Double-blind review favours increased representation of female authors. Trends in Ecology & Evolution, 23:4-6.

Abstract

Double-blind peer review, in which neither author nor reviewer identity are revealed, is rarely practised in ecology or evolution journals. However, in 2001, double-blind review was introduced by the journal Behavioral Ecology. Following this policy change, there was a significant increase in female first-authored papers, a pattern not observed in a very similar journal that provides reviewers with author information. No negative effects could be identified, suggesting that double-blind review should be considered by other journals.

http://dx.doi.org/10.1016/j.tree.2007.07.008

Urban soil habitats

Andrew.Rate — Wed, 06 Feb 2008 02:24:00 GMT

Musings on:
Byrne LB, 2007. Habitat structure: A fundamental concept and framework for urban soil ecology. Urban Ecosystems, 10:255-274.

The title's claim of a "fundamental concept and framework" are ambitious, and this paper has a few shortcomings that leave it falling somewhat short of such lofty goals. Despite this, the stated overall objective to ". . .stimulate interdisciplinary interest in, and research about . . . urbanized ecosystems" does seem to be achieved by a paper that, refreshingly, emphasises ideas over activity. And there's nothing wrong with an article having shortcomings, especially if it encourages further thought and debate.

Quotable
quote:

"In general, very little is known about the effects of
urbanization on the ecology of soils"

The article itself is an odd hybrid of original empirical data and review-based analysis and conceptualisation (but perhaps it is only an odd hybrid for soil science, a discipline whose journals seldom publish conceptual articles). The original data are used to support the concept of habitat structure in urban soil systems, by measuring various soil parameters under four treatments, which are all (lawn, old field, bark mulch, gravel mulch) manipulations of the soil surface. This is all very well . . . IF these four treatments are really types of urban habitat structure. The challenge is then to describe and preferably quantify the "habitat structure" sufficiently to be able to relate it to habitat conditions, such as soil physical and chemical properties, or to biological responses, such as species abundances or biotic fluxes such as soil respiration. Later in the article it is suggested that surface are to volume ratio is ". . .can be an appropriate description of habitat complexity", but this seems simplistic; the assumption appears to be that "complexity" is a key component of "structure". I wonder if fractal geometry might have a role in more quantitatively describing habitat complexity?

Loren Byrne makes some useful observations in this article. Like Tim Low, the point is made that ". . .human-designed plant communities may have unique and perhaps unexpected effects on urban soil biodiversity." It would certainly be interesting to test this hypothesis across a range of contrasting soils. On the other hand, there are some less-than-useful implications; the paragraph at the bottom of page 264 implies that soils are separate from "habitat structure", being ". . .beneath the different types of habitat structure. . .". A more useful approach might have been to consider soils as part of the habitat structure continuum, as soils contain spatially arranged entities of their own.

The definition of habitat structure itself, although given quite comprehensively in Table 1, may also need some work. The phrase "patterns of habitat structure", seemingly containing another level of abstraction, appears to be used synonymously with "habitat structure" in the paragraph at the bottom of p.265.

Reading back through this, I seem too critical. There is great value in this article's presentation and application of the habitat structure concept to urban soil ecosystems. There is also considerable benefit to readers, particularly postgraduate students in soil science, in examining the way the author develops and justifies arguments to present a coherent concept. As I have maintained before, the discipline of soil science and its practitioners have much to gain from a true dialogue with disciplines such as ecology and geography.

Image from "Jack and The Beanstalk" by Richard Walker and Niamh Sharkey; Barefoot Paperbacks

Year of Planet Earth

Andrew.Rate — Thu, 24 Jan 2008 03:49:00 GMT

The journal Nature is marking The Year of Planet Earth in 2008 with free access to their Year of Planet Earth feature - find it at http://www.nature.com/nature/supplements/collections/yearofplanetearth/.

Many of the articles in the feature have relevance to soil science:

From landscapes into geological history - Philip A. Allen Nature 451, 274–276 (17 January 2008) doi:10.1038/nature06586

Terrestrial ecosystem carbon dynamics and climate feedbacks - Martin Heimann & Markus Reichstein Nature 451, 289–292 (17 January 2008) doi:10.1038/nature06591

An Earth-system perspective of the global nitrogen cycle - Nicolas Gruber & James N. Galloway
Nature 451, 293–296 (17 January 2008) doi:10.1038/nature06592

Earth science and society - Frank Press Nature 451, 301–303 (17 January 2008) doi:10.1038/nature06595

Image from http://www.nature.com/nature/supplements/collections/yearofplanetearth/images/cover.jpg

Briefs

Andrew.Rate — Thu, 20 Dec 2007 03:52:00 GMT

Trevors, J.T. and Saier, M.H., Jr. (2007). Academics and their knowledge are underutilized. Water, Air and Soil Pollution, 186:1-2.

"Scientists and other academics are generally underutilized in numerous ways. For example, many scientists who also serve as instructors are not provided with the best infrastructure for use in teaching courses."

"While some academicians are utilized for governmental decision-making purposes, too often political allies are used, and almost never is a major segment of the scientific community consulted."

Schnoor, J.L. (2007). World water woes. Environmental Science & Technology, 41:7953.

"Everyone wants to live “on the edge” where seawater beckons, but it doesn’t quench our thirst. Eighty percent of Australians and more than half of all people worldwide live along the coast."
"...global warming will produce greater worldwide precipitation. But if rainfall patterns shift and floods increase, we will not benefit. By 2025, 1.8 billion people will live in countries with absolute water scarcity, according to UN estimates. Rich countries can adapt. But the future of developing countries is at stake."

Too much carbon... in soils, now?

Andrew.Rate — Thu, 01 Nov 2007 03:21:00 GMT

Musings on:
Stewart CE, Paustian K, Conant RT, Plant AF, Six A. 2007. Soil carbon saturation: concept, evidence and evaluation. Biogeochemistry 86:19-31.

On first glance I thought that this was too obvious to be significant - if carbon input fluxes (e.g. litter fall) are increased (in a single step), then of course soil carbon will increase, but asymptotically to a new maximum, caused by establishment of a new steady state with increased losses due to mineralisation, etc.
I was wrong; this simplistic understanding assumes, as Stewart et al. point out, that every increase in input flux will eventually increase soil C content. In fact, with this assumption the relationship between input flux and new equilibrium soil carbon concentration turns out to be linear; this is what most models of soil organic carbon dynamics (e.g. CENTURY or RothC) do.

Stewart et al.'s hypothesis is that with increasing input fluxes to soil, the soil C content does not keep increasing but reaches a maximum value. Using sites having a range of annual carbon inputs (0-6 Mg C/ha/y), with treatments ranging in duration from 12-51 years, they find that the data as a whole are described best by a model that assumes that soil carbon content, or at least one pool of soil carbon, reaches a limiting value.

Clearly (if correct) Stewart et al.'s findings have implications for carbon sequestration in soils for controlling CO₂ concentrations in Earth's atmosphere (again, the authors make a point of emphasising this). Soils, then, behave the same way as reforestation/revegetation in terms of carbon sequestration (ecosystems reach steady states eventually in terms of productivity vs. loss). Soil is not an infinite sink for carbon; neither is the biomass growing on it.

It's early days before this hypothesis is fully evaluated across a range of biomes, but it needs to be taken notice of. There may be some issues with the treatment of data; it wasn't clear, for example, whether clustering of data for different sites affected the fitting procedure for the carbon saturation model. But we'd better understand stuff like this if we're to be serious about exploiting the role of soils in global carbon dynamics.

Soil image from Australian Society of Soil Science Inc.

Pilgrim at Tinker Creek

Andrew.Rate — Wed, 03 Oct 2007 05:28:00 GMT

Annie Dillard, Pilgrim at Tinker Creek (1^st Perennial classics Ed. New York : HarperPerennial, 1998, 288 p. (first published 1974).

I re-read this book over the last month or so. It's wonderful - a rare book of incredible linguistic beauty. It should be compulsory reading for anyone with an interest in the natural sciences, if only to remind ourselves that the natural world was here long before the science ever was, and of our place in the scheme of things. This reading I discovered that this book (very deservedly) won the Pulitzer Prize for general non-fiction in 1975.

The quality of Annie Dillard's prose is evident from the first few paragraphs. Try this quote from p.5:

"Mountains are giant, restful, absorbent. You can heave your spirit into a mountain and the mountain will keep it, folded, and not throw it back as some creeks will. The creeks are the world with all its stimulus and beauty; I live there. But the mountains are home."

Ms Dillard generously provides an afterword, written for this edition. There are some gems here, too, perhaps well-suited to postgraduate writing, for example:

"...mathematicians do good work while they are young because as they age they suffer 'the failure of the nerve for excellence.' The phrase struck me, and I wrote it down. Nerve had never been a problem; excellence sounded novel." (p.279)

Of course, the book does not fail to discuss soils and landscapes:

"Under my spine, the sycamore roots suck watery salts. Root tips thrust and squirm between particles of soil, probing minutely; from their roving, burgeoning tissues spring infinitesimal root hairs, which affix themselves to specks of grit and sip." (p.97)

"Landscape consists in the multiple, overlapping intricacies and forms that exist in a given space at a moment in time." (p.139)

Read this book. Even if natural sciences are not your thing, I doubt you'll regret it.

Book cover image from www.librarycatalogue.act.gov.au

Globally consistent nitrogen release (backlog No. 2)

Andrew.Rate — Tue, 18 Sep 2007 01:15:00 GMT

Article for 2 July 2007:
Parton W, Silver WL, Burke IC, Grassens L, Harmon ME, Currie WS, King JY, Adair EC, Brandt LA, Hart SC, Fasth B, 2007. Global-scale similarities in nitrogen release patterns during long-term decomposition. Science 315:361-364.

Finding a global pattern in nature would be a worthy achievement for any scientist, and this is what this large team seems to have done. The research itself was truly of a global scale - a ten-year study of leaf litter decomposition with sites in most of the earth's biomes.

The similarity that the authors found was that the amount of nitrogen release and immobilization (as a fraction of total litter N) was independent of climate zone. The rate of net nitrogen release was not, however, independent of climate. N release also depended on initial N content, with consistent remaining-N vs. remaining mass of litter plots for different categories of initial N content. In fact, the initial N content was found by the authors to be "the dominant driver of net N immobilization and release ... regardless of climate" (p.364).

An interesting result was obtained when comparing data for humid and arid grasslands, where a clear difference between biomes was observed. The authors suggested that this represented the importance of photodegradation as a mechanism in arid climates (seen previously, for example, by Austin & Vivanco, 2006, who we've cited before).

In a way, the existence of a global similarity or pattern owes its existence less to the comprehensive dataset, than to the way in which the authors looked at their data. That's probably a lesson for us all...

Soil carbon review (backlog No. 1)

Andrew.Rate — Mon, 17 Sep 2007 08:21:00 GMT

This one's from 21 May 2007:
Davidson EA, Janssens IA (2006) Temperature sensitivity of soil carbon decomposition and feedbacks to climate change. Nature, 440:165-173.

A useful article on the face of it, especially in light of Article 3.4 of Kyoto which allows for carbon credits on the basis of increased soil carbon storage. It provides a good summary of many of the concepts and issues relating to carbon cycling in soils...

...but we were frustrated by a few things. Not the least some omissions and errors: for example, activation energies are not, as the authors claim (p. 165), "related to the ambient temperature..." (they create temperature dependence for chemical reactions, but do not themselves depend on temperature - Wiki). The process of carbonate weathering and formation in soils was not considered, a simplification of the idea of "soil" carbon that does not necessarily make much sense given that carbonate dissolution depends on the partial pressure of CO₂. We also felt the list of factors affecting temperature sensitivities of soil organic carbon decomposition (p. 167) was perhaps incomplete. No mention was made, either, of the observations from arid ecosystems that photodecomposition of soil organic matter may be important (see Austin AT, Vivanco L 2006 Nature 442:555-558).

The temperature-sensitivity of soil organic carbon decomposition has been contentious recently, but the authors make no firm conclusion either way, nor makes any great deductive leaps in conclusion. This may be fair enough, given the complexity of the issue. And that's perhaps what the article lacks - sufficient complexity (especially in light of the omissions). It certainly makes for good undergraduate reading, and has well-drawn and informative diagrams that will no doubt find their way into numerous lectures. But cutting-edge review? - maybe not.