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Soil Biology & Biochemistry 41 (2009) 1352–1354

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Soil Biology & Biochemistry

journal homepage: www.elsevier .com/locate/soi lb io

Letter to the Editor

Comments on the regulatory gate hypothesis and implications for C-cycling in soil

Eric Paterson*

Macaulay Institute, Soils Group, Craigiebuckler, Aberdeen AB15 8QH, Scotland, UK

a r t i c l e i n f o

Article history:Received 4 February 2009Accepted 18 February 2009Available online 4 March 2009

KeywordsRegulatory gate hypothesisPrimingSoil organic matterC-cyclingRhizodeposition

* Tel.: þ44 01224 395000; fax: þ44 01224 395010E-mail address: eric.paterson@macaulay.ac.uk

0038-0717/$ – see front matter � 2009 Elsevier Ltd.doi:10.1016/j.soilbio.2009.02.012

a b s t r a c t

The paper by Kemmitt et al. [2008. Mineralization of native soil organic matter is not regulated by thesize, activity or composition of the soil microbial biomass – a new perspective. Soil Biology andBiochemistry 40, 61–73] proposing the existence of an abiotic regulatory gate that controls the rate-limiting step of stabilised soil organic matter (SOM) mineralization, has initiated a fundamental and far-reaching debate. In this contribution the implications of a functioning abiotic regulatory gate areconsidered in the context of microbial community diversity and soil carbon cycling. I argue that althoughthe evidence presented in support of the regulatory gate is strong, abiotic routes for SOM-mineralizationfunction in parallel with biologically mediated mechanisms. Evidence is now accumulating that, in thepresence of plant-inputs to soil, enhanced microbial mobilisation of SOM into biomass is a quantitativelyimportant and ubiquitous process. I argue that this mineralization of SOM is fuelled by energy-richsubstrates and is driven by microbial nutrient-demand. This implies that the mineralization of stabilisedSOM and the turnover of C-inputs from current vegetation are intimately linked through the functioningof microbial communities associated with plants. This suggests that the microbial ‘eye of the needle’ isa crucial control-point in determining the carbon balance of soils. Fortunately, there are now excellentmethods that allow quantification of SOM- and plant-derived C-fluxes through the members of soilmicrobial communities, and will also allow quantification of the relative importance of the abiotic andbiotic routes of SOM-mineralization.

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1. Background

In their recent paper published in Soil Biology & Biochemistry,‘Mineralization of native soil organic matter is not regulated by thesize, activity or composition of the soil microbial biomass- A newperspective’, Kemmitt et al. (2008) proposed the hypothesis that therate-limiting step of soil organic matter (SOM) mineralization isabiotic. This is in direct opposition to the prevailing view thatmicrobial populations differ in their physiological abilities tometabolise recalcitrant organic matter (Killham, 1994) and thatfactors increasing microbial activity, such as availability of labile C-sources, are associated with elevated rates of SOM-mineralization(Kuzyakov et al., 2000). The positing of the abiotic view of SOM-mineralization came from the interpretation of a series of elegantlyconstructed experiments in which drastic perturbation of the soilmicrobial community (chloroform fumigation) did not affect thesubsequent rates of SOM-mineralization (Kemmitt et al., 2008).Their entirely reasonable conclusion from these experiments wasthat if microbial biomass can be reduced greatly (>90%), concurrent

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with elimination of a large proportion of component populations,and mineralization of SOM is still largely unaffected, then microbialcommunities cannot be responsible for the rate-limiting step ofSOM-mineralization.

2. Potential implications

If correct, the implications of an abiotic ‘regulatory gate’ thatmediates fluxes of C and nutrients from recalcitrant SOM to formsavailable to microbes and plants are profound. Perhaps the mostobvious implication would be for our conceptual view of microbialcommunities and the role of species and functional diversity inorganic matter transformations. Current theories of soil microbialecology consider microbial populations to have differing growthstrategies, which for simplicity can be characterised as zymogenousand autochthonous, adapted to utilisation of transient, labile orpersistent, recalcitrant organic matter sources, respectively(Kuzyakov et al., 2009). It is known that soil microbial communitieshave a very high species diversity and that the loss of a single (oreven many) species from a community may not affect the rates ofsoil processes, which has led to the concept of functional redun-dancy in microbial communities (Nannipieri et al., 2003).

E. Paterson / Soil Biology & Biochemistry 41 (2009) 1352–1354 1353

In their response to the original paper, Kuzyakov et al. (2009)suggest that the functional redundancy in autochthonouscommunities may explain the maintenance of SOM-mineralizationfollowing chloroform fumigation. However, as noted in theresponse by Brookes et al. (2009), this explanation seemsimprobable given the severity of the fumigation treatment onmicrobial communities. Another ‘biological’ mechanism by whichrates of SOM-mineralization could be maintained in fumigated soilswould be the persistence of enzyme activity through stabilizationof the enzyme complement of the previous, larger and morediverse microbial community (Kuzyakov et al., 2009). Althoughproteins, particularly those of microbial origin, may persist in soilsfor considerable periods (Rillig et al., 2007), the maintenance ofpre-fumigation SOM-mineralizing functions would be a striking,and in my view an improbable, uncoupling of soil biologicalactivities and functions. In effect, this view of soil enzymes wouldimply that current soil functions were a cumulative product ofprevious functions and largely independent of current microbialactivity. Therefore, on weight of evidence, the results of Kemmittet al. (2008) are consistent with the supply of organics to themicrobial community being independent of microbially-drivenprocesses. The logical extension to this conclusion is that thechemical complexity and heterogeneity of SOM is not a driver ofmicrobial species diversity, with microbial communities sustainedon abiotically mobilised ‘packets’ of SOM and the (chemically)predictable inputs from plants.

In my view, the regulatory gate hypothesis has a second impli-cation of perhaps even greater potential importance. That is, ifSOM-mineralization is unaffected by microbial activity, then theinference is that the processes of rhizodeposition and the subse-quent biological processing of these inputs through the soil biotaare uncoupled from processes driving C-outputs from stabilisedSOM. If correct, one consequence of inputs being uncoupled frommineralization of soil SOM stocks would be that C-sequestrationcould be increased simply by management to promote inputs(assuming that physicochemical conditions governing the regula-tory gate were unaffected). As net inputs to soil from plants can bemeasured much more easily than the net C-balance of soils (Sabyet al., 2008), this would greatly simplify research efforts in whatremains a poorly characterised, but quantitatively important, partof the global C-cycle.

So, in the context of soil C-cycling, does the regulatory gatehypothesis clear away the mire of complexity that obscures solu-tions to seemingly straight-forward questions, such as whethera soil is accumulating or losing C? As I will argue, in my view theanswer is ‘no’, but the proponents of the regulatory gate haveachieved their aim of stimulating much needed debate, and inaddition have opened-up new avenues for research. It is quiteremarkable, and hugely inspiring, that such fundamental andimportant issues in soil science are still up for debate and are at lastbecoming tractable problems.

3. Importance of linking input and output processes in soils

The experiments reported on by Kemmitt et al. (2008) andprevious publications on the development of fumigation–incuba-tion as an assay for microbial biomass size, involve soil incubationsin the absence of plants or other sources of C-inputs. In criticisingthe concept of abiotic control of SOM-mineralization Kuzyakovet al. (2009) cite the widely reported phenomenon of priming,where labile substrate additions to soil (e.g. rhizodeposition)stimulate SOM-mineralization (Allard et al., 2006). I agree with thisline of criticism against the generality of abiotic control of SOM-mineralization. I also agree that priming can be demonstratedunequivocally and quantified accurately through application of

isotope labelling and tracking approaches (Paterson et al., 2008).For priming associated with root activity it is possible to envisageeffects that are mediated by processes that are not incompatiblewith the regulatory gate hypothesis (e.g. disruption of aggregates ormovement of SOM-derived C in mass flow of water). However,there are also many studies that have identified priming wheresubstrates have been applied to soil directly and significant effectson physicochemical conditions are difficult to envisage.

In their response to Kuzyakov et al. (2009), Brookes et al. (2009)dismiss priming effects as transient processes, certainly incomparison with the turnover of SOM, inferring that their influenceon SOM dynamics is negligible. It is very difficult to accept thisview. The influence of intense exudation from a root tip on a fewmm3 of soil may be transient as the root extends through it, buta 10 cm3 volume of grassland soil may contain 200 m of root lengthexuding rhizodeposits and undergoing tissue turnover (Gregory,2006). Therefore, although organic inputs to soil are heterogeneousin time and space, they are a constant influence on vegetated soil.

4. Factors limiting microbial growth and activity

To reconcile the strong evidence for the abiotic regulatory gatewith that for biologically mediated priming of SOM it is useful toconsider the limitations to microbial growth in soils. Kemmitt et al.(2008), correctly in my view, consider the microbial communitiesin their flask incubations to be C (and energy) limited. They alsoconvincingly argue that the complex and heterogeneous structureof humified SOM make it nonviable as a C-source (i.e. it requiresmore energy to make it available than can be gained from its uti-lisation). They also make the point that if this was not the case (andmicrobial populations were physiologically capable of its break-down), SOM would be depleted at an increasingly rapid rate as theutilising organisms proliferated. It is evident that this is not howSOM dynamics function in soils.

In contrast to bulk soil, in the rhizosphere and the other hot-spots for microbial activity identified by Kuzyakov et al. (2009),microorganisms are likely to be nutrient limited, and relatively C-replete. Under these circumstances the issue for microorganismsceases to be whether mineralization of SOM is cost-effective forenergy generation, but rather whether the excess energy availableto them can be utilised to harvest limiting nutrients from SOM. Forplants which are generally not C-limited, the release of rhizode-posits may be an effective means to exploit the abilities of therhizosphere microbiota to access nutrients from SOM, with thesenutrients ultimately becoming available to the plant through thetrophic interactions of the microbial loop (Paterson, 2003). Indeed,there is now increasing evidence that mycorrhizal fungi facilitateplant access to SOM nutrient sources (Talbot et al., 2008), where theplant is clearly fuelling the fungal exploitation of SOM. It is possiblethat this is a specific example of a phenomenon more broadlyapplicable to the free-living microbiota associated with plants. Thisis not a new idea, but is one that has been difficult to prove,however, evidence is now accumulating in support of it (e.g.Hamilton et al., 2008). In our own work, we have quantifiedmicrobial use of plant- and SOM-C in the rhizosphere, usingcontinuous 13C-labelling to distinguish C-sources (Paterson et al.,2007). One of the most surprising outcomes from this research wasthat even within the rhizosphere, SOM-derived C contributeda quantitatively important proportion of the microbial biomass.Given the relatively high turnover of rhizosphere microbialbiomass, this incorporation of SOM-C represents significant, bio-logical mobilisation of SOM. This was confirmed by quantifyingSOM-mineralization (via partitioning of soil respiration into plantand SOM sources), which indicated that SOM-mineralizationincreased with increasing plant growth (Paterson et al., 2008).

E. Paterson / Soil Biology & Biochemistry 41 (2009) 1352–13541354

Despite these experiments being done in disturbed soils (poten-tially making SOM-C more available to microorganisms), the resultspoint to there being a tight coupling of microbial processing ofplant- and SOM-derived C-sources. The finding that SOM-derived Cis an important source to plant-associated, zymogenous microbialgroups has been consistently reported in other studies, suggestingthat co-metabolism of C-sources is a general phenomenon (Pelzet al., 2005; Kramer and Gleixner, 2006). Indeed a recent study hassuggested that rather than promoting C-sequestration, increasedplant-derived inputs to soil as a consequence of global change mayactually induce net loss of SOM (Carney et al., 2007).

5. Ways forward

The regulatory gate hypothesis has highlighted the uncertaintiessurrounding microbial functioning in relation to soil C-cycling. Iagree with Kuzyakov et al. (2009) that isotopic labelling providesopportunities to discriminate and quantify processes, sheddinglight on this issue. Further, there are significant advantages in thiscontext to applying quantitative labelling, i.e. homogenous label-ling of fluxes as opposed to use of non-quantitative tracers,allowing quantification of C-source fluxes into the key labile poolsof DOC/DON and the microbial biomass. These approaches aresufficient to identify the involvement (if any) of microbialcommunities in regulating the rate of SOM-mineralization. AsKemmitt et al. (2008) have apparently demonstrated the func-tioning of an abiotic pathway for SOM-mineralization, the methodswill also allow quantification of the relative importance of bioticand abiotic fluxes from SOM, and how this varies as functions ofspatial location (e.g. soil depth) and time (e.g. seasonality of plantgrowth).

If the importance of the microbial biomass in SOM-mineraliza-tion is (re)confirmed, then continued investigation of the role ofmicrobial diversity in C-cycling in the context of soil organic matterstocks and exchange with atmospheric C-pools will be a justifiedpriority. It has long been recognised that the microbial biomass isthe ‘eye of the needle’ through which C and nutrients flow; and aretransformed (Jenkinson, 1977). There is now increasing evidencethat the flows of C into soil from plants are intimately linked withthe flows out of it from SOM, coupled by the activities of theorganisms that comprise the ‘eye of the needle’. Developing anunderstanding of the microbial ecology of these linked C-flows isnow supported by methods that allow examination of the activitiesof distinct microbial groups, as opposed to treating the microbialbiomass as a single, unstructured entity. To borrow anothercommon soil science analogy, application of these techniques isakin to picking the lock of the ‘black box’, rather than shaking itroughly and trying to listen to what is inside.

At a broad scale, use of PLFA biomarkers is a useful and estab-lished method to link microbial groups to C-cycling processes,whilst other methods offer increasingly detailed dissection of themicrobial biomass and its functions. Application of nucleic acidstable isotope probing offers the potential for species-specificdelineation of microbial roles, if the variants of this approach cancircumvent current problems with density separation of 13C-labelled nucleic acids. Microarray approaches may allow charac-terisation of microbial gene expression which will be useful, forexample, in determining factors regulating exoenzyme productionin rhizosphere bacteria. Proteomics offers the potential to identifythe functions and source organisms for enzymes in soil (Schulze,2005; Schulze et al., 2005), with the added benefit that proteinsoffer the potential to simultaneously track fluxes of C, N and P, ifcoupled to labelling approaches. Therefore, the debate reignited by

Kemmitt et al. (2008) provides a welcome focus for studies of soil C-cycling, which will fortunately be supported by developing meth-odologies that offer the potential to resolve the uncertainties withever increasing accuracy and detail.

Acknowledgement

This work was funded by the Scottish Government’s Rural andEnvironmental Research and Analysis Directorate.

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