Paper out: Micro-scale determinants of bacterial diversity in soil

A review paper I wrote with former colleagues at the Netherlands Institute of Ecology (Alexandra Wolf, Sarah Jennings and George Kowalchuk) has come out in FEMS Microbiology reviews: website (cough, cough). Scientists should be happy when the fruits of their labour are published, but I never really enjoy a paper coming out, as I am mainly focused on inevitable small mistakes and papers I should have cited but didn’t. Anyway, it is now out in the open for the whole world to scrutinize.

The topic of this review is the largely hidden lives that bacteria live underneath our feet. Soil is a strange habitat. On one hand it is chock full of bacteria (often hundreds of millions of cells per gram), but on the other hand, the fine-grained nature of soils means that the total surface area of a cubic centimetre is very large, resulting in a very low percentage of surface area actually covered with bacteria (Young and Crawford estimate only a millionth of a percent). Not only are individual bacteria or (micro)colonies separated by relatively large distances, soil is a complex matrix of pores that are only partially filled with water. Those pores not filled with water but with gases form a great barrier to bacterial dispersal and to the exchange of signals and food. This highly heterogeneous distribution will have a profound effect on species interactions, and species interactions in turn are likely to have a profound effect on species diversity. Besides discussing some of the hypotheses on how this spatial structure might promote the high diversity that is observed in soil (for example, more than 33,000 taxa could be detected in a single soil sample using a Phylochip), we also review the methods that can be used to test these hypotheses.


Examples of methods visualizing bacterial microhabitats. (a) Fungal hypha within the complex three-dimensional soil matrix. Image collected with FEI Quanta 200 field emission Environmental SEM from field-wet soil [SJJ and Research Centre for Surface and Material Science (RCSMS) unpublished data]. (b) A composite elemental distribution map [oxygen (green), silica (red), and potassium (blue)], obtained via energy dispersive spectroscopy (EDAX Pegasus EDS detector) for a resin-embedded soil aggregate (SJJ and RCSMS, unpublished data). (c) Pseudomonas aeruginosa SG81 biofilm formed on Nafion grains after live/dead staining (adapted from Leis et al., 2005). Cells with a damaged cell membrane appear red, while cells with intact membranes are green. (d) Pore network of a sand sample, obtained via micro-computed tomography (μCT) (ABW and Wilfried Otten, University of Abertay Dundee).

Apart from their small size, which makes it hard to study bacteria in general, soil has the problem that it is opaque, hindering observation using microscopy. Another problem is that soil is highly structured, and so taking a sample that preserves the natural spatial configuration of cells is very hard. Compromises thus will have to be made, trading of biological realism with experimental rigor. In the paper, we discuss some exciting new experimental approaches, including the use of microfluidic devices and using artificial ‘see-through’ soil particles.

We conclude that the use of novel methodologies, appreciation of a large body of older soil structure literature and the integration of insights from microbial and ‘macrobial’ ecology together will be necessary to help us understand what forces shape bacterial diversity at the micro-scale and more specifically inform us how natural processes are modified by human management practices. Is bacterial migration affected by tillage practices or increased human travel? Does lowered connectivity through groundwater depletion affect bacterial interactions? Are we losing soilborne bacterial diversity and does it affect soil ecosystem services? The answers to such grand questions could well be found at the very smallest scales.*


* I am afraid I have to take full responsibility for the cheesy pay-off line…

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