Soil Science Journal Club : ecology

Urban Soils

Andrew.Rate — Wed, 25 Feb 2009 02:20:00 GMT

The journal Urban Ecosystems has just published a Special Issue on Soils. As our planet and its human populations become increasingly urbanised, this would seem to be a growth area for the earth and ecological sciences.

Some of the articles from this issue of the journal:

A comparison of soil organic carbon stocks between residential turf grass and native soil
Richard V. Pouyat, Ian D. Yesilonis and Nancy E. Golubiewski
Altered resources, disturbance, and heterogeneity: A framework for comparing urban and non-urban soils
S. T. A. Pickett and M. L. Cadenasso
Scratching the surface and digging deeper: exploring ecological theories in urban soils
Mitchell A. Pavao-Zuckerman and Loren B. Byrne
Urban soil ecology as a focal point for environmental education
E. A. Johnson and K. M. Catley

I'm definitely looking forward to reading some of these.

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

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

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.

The New Nature

Andrew.Rate — Thu, 30 Aug 2007 01:58:00 GMT

Just read Tim Low's book...

Low, Tim. 2003. The New Nature. Penguin Books Australia.

Overall the thesis of this book seems to be that nature includes humans - whether we like it or not, we're intimately involved in ecosystems -and therefore what humans have done and will do needs to be factored into our understanding of "nature".

Recurrent ideas (bursting some sacred balloons)

human activities and disturbance of ecosystems / creation of new ones (urbanisation, agriculture) can benefit many species including some endangered ones;
"wilderness" as a concept does not really exist (but is more likely based on wishful thinking);
animals can be as destructive as humans (sometimes because human activity forces them into different or more crowded spaces);
some conservation practices have been damaging (e.g., reintroductions, focusing only on few [animal] species); culling (of animals and plants) may be necessary;
we favour the adaptable species over the niche dwellers...

And why is this book discussed on a Soil Science blog? Mostly because I wanted to (and enjoyed the book), but Tim Low does discuss the impact of the "new nature" on soils, if not soil functioning, as in the following quotes:

p. 53 - "Seabirds evidently bred colonially back in Jurassic times, and dinosaurs in the Triassic era, which means that soil pollution dates back 200 million years."

p. 305 - "... nature as the sum total of wild plants and animals, with rocks, soil, water, weather and tectonic forces often thrown in."

p. 228 - "Multiplying kangaroos cop the blame for many crimes. I've heard them accused of destroying endangered plants, eroding soil, eliminating the understorey, preventing regeneration, degrading habitat for birds, and encouraging invasive native plants and birds."