Is soil carbon disappearing? The dynamics of soil organic carbon in Java

Research in the soil of the tropics mostly has demonstrated the decline of soil organic carbon (SOC) after conversion of primary forest to plantation and cultivated lands. This paper illustrates the dynamics of SOC on the island of Java, Indonesia, from 1930 to 2010. We used 2002 soil profile observations containing organic carbon (C) analysis in the topsoil, which were collected by the Indonesian Center for Agricultural Land Resources Research & Development from 1923 to 2007. Results show the obvious decline of SOC values from around 2% in 1930–1940 to 0.8% in 1960–1970. However, there has been an increase of SOC content since 1970, with a median level of 1.1% in the year 2000. Our analysis suggests that the human influence and agricultural practices on SOC in Java have been a stronger influence than the environmental factors. SOC for the top 10 cm has shown a net accumulation rate of 0.2–0.3 Mg C ha^?1 yr^?1 during the period 1990–2000. These findings give rise to optimism for increased soil C sequestration in the tropics.     

Is the shoot a root with a view?

Recently, it has been shown that the same sets of genes act in both root and shoot to regulate cell fate and patterning. One gene cassette regulates epidermal cell fate, another cassette regulates ground tissue derived cell fate and organization. Ectopic expression and laser ablation have been used to probe the mechanisms by which these genes perform their tissue and organ-specific functions.     

Brown ground: a soil carbon analogue for the green world hypothesis?

For many decades, ecologists have asked what prevents herbivores from consuming most of the plant biomass in terrestrial ecosystems, or "Why is the world green?" Here I ask the analogous question for detritivores: what prevents them from degrading most of the organic material in soils, or "Why is the ground brown?" For fresh plant detritus, constraints on decomposition closely parallel constraints on herbivory: both herbivore and decomposer populations may be controlled by plant tissue chemistry from the bottom up and predators from the top down. However, the majority of soil carbon is not plant litter but carbon that has been consumed by detritivores and reprocessed into humic compounds with complex and random chemical structures. This carbon persists mainly because the chemical properties of humic compounds and interactions with soil minerals constrain decomposition by extracellular enzymes in soil. Other constraints on decomposers, such as nutrient limitation of enzyme production and competition with opportunistic microbes, also contribute to brown ground. Ultimately, the oldest soil carbon persists via transformation into complex molecules that are impervious to enzymatic attack and effectively decoupled from processing by the soil food web.     

The root microbiota—a fingerprint in the soil?

Background

The root system of a plant is known to host a wide diversity of microbes that can be essential or detrimental to the plant. Microbial ecologists have long struggled to understand what factors structure the composition of these communities. An overlooked part of the microbial community succession in root systems has been the potential for individual variation among plants shaped by early colonisation events such as microbial exposure of the seed inside the parent plant and during dispersal.

Scope

In this review we outline life events of the plant that can affect the composition of its root microbiota and relate ecological theory of community assembly to the formation of the root microbiota.

Conclusion

All plants are exposed to environmental conditions and events throughout their lifetime that shape their phenotype. The microbial community associated with the plant is ultimately an extension of this phenotype. Therefore, only by following a plant from its origin inside the flower to senescence, can we fully understand how the associated microbial community was assembled and what determined its composition.     

Is leaf dry matter content a better predictor of soil fertility than specific leaf area?

Background and Aims

Specific leaf area (SLA), a key element of the ‘worldwide leaf economics spectrum’, is the preferred ‘soft’ plant trait for assessing soil fertility. SLA is a function of leaf dry matter content (LDMC) and leaf thickness (LT). The first, LDMC, defines leaf construction costs and can be used instead of SLA. However, LT identifies shade at its lowest extreme and succulence at its highest, and is not related to soil fertility. Why then is SLA more frequently used as a predictor of soil fertility than LDMC?

Methods

SLA, LDMC and LT were measured and leaf density (LD) estimated for almost 2000 species, and the capacity of LD to predict LDMC was examined, as was the relative contribution of LDMC and LT to the expression of SLA. Subsequently, the relationships between SLA, LDMC and LT with respect to soil fertility and shade were described.

Key Results

Although LD is strongly related to LDMC, and LDMC and LT each contribute equally to the expression of SLA, the exact relationships differ between ecological groupings. LDMC predicts leaf nitrogen content and soil fertility but, because LT primarily varies with light intensity, SLA increases in response to both increased shade and increased fertility.

Conclusions

Gradients of soil fertility are frequently also gradients of biomass accumulation with reduced irradiance lower in the canopy. Therefore, SLA, which includes both fertility and shade components, may often discriminate better between communities or treatments than LDMC. However, LDMC should always be the preferred trait for assessing gradients of soil fertility uncoupled from shade. Nevertheless, because leaves multitask, individual leaf traits do not necessarily exhibit exact functional equivalence between species. In consequence, rather than using a single stand-alone predictor, multivariate analyses using several leaf traits is recommended.     

A root is a root is a root? Water uptake rates of Citrus root orders

Knowledge about the physiological function of root orders is scant. In this study, a system to monitor the water flux among root orders was developed using miniaturized chambers. Different root orders of 4‐year‐old Citrus volkameriana trees were analysed with respect to root morphology and water flux. The eight root orders showed a broad overlap in diameter, but differences in tissue densities and specific root area (SRA) were clearly distinguishable. Thirty per cent of the root branch biomass but 50% of the surface area (SA) was possessed by the first root order, while the fifth accounted for 5% of the SA (20% biomass). The root order was identified as a determinant of water flux. First‐order roots showed a significantly higher rate of water uptake than the second and third root orders, whereas the fourth and fifth root orders showed water excess. The water excess suggested the occurrence of hydraulic redistribution (HR) as a result of differences in osmotic potentials. We suggest that plants may utilize hydraulic redistribution to prevent coarse root desiccation and/or to increase nutrient acquisition. Our study showed that the novel ‘miniature depletion chamber’ method enabled direct measurement of water fluxes per root order and can be a major tool for future studies on root order traits.     

Initial soil organic carbon stocks govern changes in soil carbon: Reality or artifact?

Changes in soil organic carbon (SOC) storage have the potential to affect global climate; hence identifying environments with a high capacity to gain or lose SOC is of broad interest. Many cross-site studies have found that SOC-poor soils tend to gain or retain carbon more readily than SOC-rich soils. While this pattern may partly reflect reality, here we argue that it can also be created by a pair of statistical artifacts. First, soils that appear SOC-poor purely due to random variation will tend to yield more moderate SOC estimates upon resampling and hence will appear to accrue or retain more SOC than SOC-rich soils. This phenomenon is an example of regression to the mean. Second, normalized metrics of SOC change—such as relative rates and response ratios—will by definition show larger changes in SOC at lower initial SOC levels, even when the absolute change in SOC does not depend on initial SOC. These two artifacts create an exaggerated impression that initial SOC stocks are a major control on SOC dynamics. To address this problem, we recommend applying statistical corrections to eliminate the effect of regression to the mean, and avoiding normalized metrics when testing relationships between SOC change and initial SOC. Careful consideration of these issues in future cross-site studies will support clearer scientific inference that can better inform environmental management.     

Cultivation of a perennial grass for bioenergy on a boreal organic soil – carbon sink or source?

The area under the cultivation of perennial bioenergy crops on organic soils in the northern countries is fast increasing. To understand the impact of reed canary grass (RCG, Phalaris arundinaceae L.) cultivation on the carbon dioxide (CO₂) balance of an organic soil, net ecosystem CO₂ exchange (NEE) was measured for four years in a RCG cultivated cutover peatland in eastern Finland using the eddy covariance technique. There were striking differences among the years in the annual precipitation. The annual precipitation was higher during 2004 and 2007 and lower during 2005 and 2006 than the 1971–2000 regional mean. During wet growing seasons, moderate temperatures, high surface soil moisture and low evaporative demand favoured high CO₂ uptake. During dry seasons, owing to soil moisture and atmospheric stress, photosynthetic activity was severely restricted. The CO₂ uptake [gross primary productivity (GPP)] was positively correlated with soil moisture, air temperature and inversely with vapour pressure deficit. Total ecosystem respiration (TER) increased with increasing soil temperature but decreased with increasing soil moisture. The relative responses of GPP and TER to moisture stress were different. While changes in TER for a given change in soil moisture were moderate, variations in GPP were drastic. Also, the seasonal variations in TER were not as conspicuous as those in GPP implying that GPP is the primary regulator of the interannual variability in NEE in this ecosystem. The ecosystem accumulated a total of 398 g C m^?2 from the beginning of 2004 until the end of 2007. It retained some carbon during a wet year such as 2004 even after accounting for the loss of carbon in the form of harvested biomass. Based on this CO₂ balance analysis, RCG cultivation is found to be a promising after‐use option on an organic soil.     

Is there a future for GMOs?

Despite strict regulation and a clean safety record, research and development of genetically modified (GM) crops and other organisms has been confronted with tremendous public hostility. Why has this happened, and how can scientists try to guide the debate into more rational channels? The answers may determine the future of GM technology and our ability to provide for a growing world population.     

Can root electrical capacitance be used to predict root mass in soil?

Background

Electrical capacitance, measured between an electrode inserted at the base of a plant and an electrode in the rooting substrate, is often linearly correlated with root mass. Electrical capacitance has often been used as an assay for root mass, and is conventionally interpreted using an electrical model in which roots behave as cylindrical capacitors wired in parallel. Recent experiments in hydroponics show that this interpretation is incorrect and a new model has been proposed. Here, the new model is tested in solid substrates.

Methods

The capacitances of compost and soil were determined as a function of water content, and the capacitances of cereal plants growing in sand or potting compost in the glasshouse, or in the field, were measured under contrasting irrigation regimes.

Key Results

Capacitances of compost and soil increased with increasing water content. At water contents approaching field capacity, compost and soil had capacitances at least an order of magnitude greater than those of plant tissues. For plants growing in solid substrates, wetting the substrate locally around the stem base was both necessary and sufficient to record maximum capacitance, which was correlated with stem cross-sectional area: capacitance of excised stem tissue equalled that of the plant in wet soil. Capacitance measured between two electrodes could be modelled as an electrical circuit in which component capacitors (plant tissue or rooting substrate) are wired in series.

Conclusions

The results were consistent with the new physical interpretation of plant capacitance. Substrate capacitance and plant capacitance combine according to standard physical laws. For plants growing in wet substrate, the capacitance measured is largely determined by the tissue between the surface of the substrate and the electrode attached to the plant. Whilst the measured capacitance can, in some circumstances, be correlated with root mass, it is not a direct assay of root mass.     

Is dipalmitoylphosphatidylcholine a substrate for convertase?

Convertase has homology with carboxylesterases, but its substrate(s) is not known. Accordingly, we determined whether dipalmitoylphosphatidylcholine (DPPC), the major phospholipid in surfactant, was a substrate for convertase. We measured [(3)H]choline release during cycling of the heavy subtype containing [(3)H]choline-labeled DPPC with convertase, phospholipases A(2), B, C, and D, liver esterase, and elastase. Cycling with liver esterase or peanut or cabbage phospholipase D produced the characteristic profile of heavy and light peaks observed on cycling with convertase. In contrast, phospholipases A(2), B, and C and yeast phospholipase D produced a broad band of radioactivity across the gradient without distinct peaks. [(3)H]choline was released when natural surfactant containing [(3)H]choline-labeled DPPC was cycled with yeast phospholipase D but not with convertase or peanut and cabbage phospholipases D. Similarly, yeast phospholipase D hydrolyzed [(3)H]choline from [(3)H]choline-labeled DPPC after incubation in vitro, whereas convertase, liver esterase, or peanut and cabbage phospholipases D did not. Thus convertase, liver esterase, and plant phospholipases D did not hydrolyze choline from DPPC either on cycling or during incubation with enzyme in vitro. In conclusion, conversion of heavy to light subtype of surfactant by convertase may require a phospholipase D type hydrolysis of phospholipids, but the substrate in this reaction is not DPPC.     

Is a constant low-entropy process at the root of glycolytic oscillations?

We measured temporal oscillations in thermodynamic variables such as temperature, heat flux, and cellular volume in suspensions of non-dividing yeast cells which exhibit temporal glycolytic oscillations. Oscillations in these variables have the same frequency as oscillations in the activity of intracellular metabolites, suggesting strong coupling between them. These results can be interpreted in light of a recently proposed theoretical formalism in which isentropic thermodynamic systems can display coupled oscillations in all extensive and intensive variables, reminiscent of adiabatic waves. This interpretation suggests that oscillations may be a consequence of the requirement of living cells for a constant low-entropy state while simultaneously performing biochemical transformations, i.e., remaining metabolically active. This hypothesis, which is in line with the view of the cellular interior as a highly structured and near equilibrium system where energy inputs can be low and sustain regular oscillatory regimes, calls into question the notion that metabolic processes are essentially dissipative.     

How long before a change in soil organic carbon can be detected?

When planning sampling in an experiment where soil organic carbon (SOC) content is expected to change, it is necessary to know how many samples will need to be taken to demonstrate a change in SOC and after how long this change will be detectable. Much has been published on the number of samples required to demonstrate the minimum detectable difference in SOC, but less on how long it takes for this change to be detectable. In this paper, a model of SOC dynamics is used to estimate the minimum time taken for a change in total SOC content to become measurable under different carbon inputs, land uses and soil types. For free air carbon dioxide enrichment (FACE), and other experiments in which SOC is expected to increase, relationships between the percentage change in C inputs and the time taken to measure a change in SOC are presented, for two levels of sampling intensity corresponding to the maximum that is practically possible in most experiments (～100 samples) and that used regularly in field experiments (10–20 samples). In FACE experiments, where C inputs increase by a maximum of about 20–25%, SOC change could be detected with 90% confidence after about 6–10 years if a sampling regime allowing 3% change in background SOC level (probably requiring a very large number of samples) were used, but could not be detected at all if a sampling regime were used that allowed only a 15% change in background SOC to be detected. If increases in C inputs are much below 15%, it might not be possible to detect a change in soil C without an enormous number of samples. Relationships between the change in C inputs and the time taken to measure a change in SOC are robust over a range of soil types and land uses. The results demonstrate how models of SOC dynamics can be used to complement statistical power analyses for planning when, and how intensively, to sample soils during experiments. An advantage of the modelling approach demonstrated here is that estimates of the minimum time taken for a change in soil carbon to become detectable can be made, even before any detailed soil samples are taken, simply from estimates of the likely increase in carbon inputs to the soil (via expected changes in net primary production).     

Carbon flow in the rhizosphere: carbon trading at the soil–root interface

The loss of organic and inorganic carbon from roots into soil underpins nearly all the major changes that occur in the rhizosphere. In this review we explore the mechanistic basis of organic carbon and nitrogen flow in the rhizosphere. It is clear that C and N flow in the rhizosphere is extremely complex, being highly plant and environment dependent and varying both spatially and temporally along the root. Consequently, the amount and type of rhizodeposits (e.g. exudates, border cells, mucilage) remains highly context specific. This has severely limited our capacity to quantify and model the amount of rhizodeposition in ecosystem processes such as C sequestration and nutrient acquisition. It is now evident that C and N flow at the soil–root interface is bidirectional with C and N being lost from roots and taken up from the soil simultaneously. Here we present four alternative hypotheses to explain why high and low molecular weight organic compounds are actively cycled in the rhizosphere. These include: (1) indirect, fortuitous root exudate recapture as part of the root’s C and N distribution network, (2) direct re-uptake to enhance the plant’s C efficiency and to reduce rhizosphere microbial growth and pathogen attack, (3) direct uptake to recapture organic nutrients released from soil organic matter, and (4) for inter-root and root–microbial signal exchange. Due to severe flaws in the interpretation of commonly used isotopic labelling techniques, there is still great uncertainty surrounding the importance of these individual fluxes in the rhizosphere. Due to the importance of rhizodeposition in regulating ecosystem functioning, it is critical that future research focuses on resolving the quantitative importance of the different C and N fluxes operating in the rhizosphere and the ways in which these vary spatially and temporally.     

Is growth of soil microorganisms in boreal forests limited by carbon or nitrogen availability?

To study whether the biomass of soil microorganisms in a boreal Pinus sylvestris-Vaccinium vitis-idaea forest was limited by the availability of carbon or nitrogen, we applied sucrose from sugar cane, a C₄ plant, to the organic mor-layer of the C₃–C dominated soil. We can distinguish between microbial mineralization of the added sucrose and respiration of endogenous carbon (root and microbial) by using the C₄-sucrose as a tracer, exploiting the difference in natural abundance of ¹³C between the added C₄-sucrose (¹³C –10.8) and the endogenous C₃–carbon (¹³C –26.6 ). In addition to sucrose, NH₄Cl (340 kg N ha^–1) was added factorially to the mor-layer. We followed the microbial activity for nine days after the treatments, by in situ sampling of CO₂ evolved from the soil and mass spectrometric analyses of ¹³C in the CO₂. We found that microbial biomass was limited by the availability of carbon, rather than nitrogen availability, since there was a 50% increase in soil respiration in situ between 1 h and 5 days after adding the sucrose. However, no further increase was observed unless nitrogen was also added. Analyses of the ¹³C ratios of the evolved CO₂ showed that increases in respiration observed between 1 h and 9 days after the additions could be accounted for by an increase in mineralization of the added C₄–C.