To successfully reduce atmospheric CO2 by sequestering additional soil carbon, it is essential to understand the potential of a given soil to store carbon in a stable form. Carbon that has formed organo-mineral complexes with silt and clay particles is believed to be less susceptible to decay than non-complexed, or particulate, organic carbon. Using direct measurements of mineral associated organic matter (MAOC) on a subset of samples, and an approach developed previously for primarily allophanic soils, we took a modeling approach to estimate MAOC for 537 samples of much coarser and younger soils from 99 non-cultivated and agricultural sites in the Okanagan Valley, British Columbia, Canada. Using specific surface area (SSA) or soil texture as indicators of the mineral surface area available for sorption of organic matter, we used both Random Forest (RF) and Stepwise Multiple Regression with Akaike Information Criterion (SMR) to determine a best fit model for predicting MAOC. Random Forest modeling using SSA in addition to total SOC, exchangeable calcium, exchangeable potassium, and soil pH performed better than SMR for determining MAOC in these soils (R2: 0.790 for RF; R2: 0.713 for SMR). To determine if a MAOC deficit existed for these soils, we then applied a quantile regression approach wherein the predicted 90th quantile of MAOC represents the MAOC formation capacity. We determined that MAOC deficits were present in all soils and increased with depth. Moreover, clay rich soils had greater MAOC deficits (1.62 g kg−1 for 0–15 cm, 4.01 g kg−1 for 15–30 cm, and 5.80 g kg−1 for 30–60 cm), than sandier soils (1.01 g kg−1 for 0–15 cm, 2.72 g kg−1 for 15–30 cm, and 3.69 g kg−1 for 30–60 cm). Furthermore, the upper 30 cm of these soils have the potential to increase MAOC stocks by 29% (48.0 million kg of MAOC over 8,501 ha) before they reach formation capacity. This study highlights the variability in MAOC formation capacity of soils with different physicochemical properties and provides a framework for estimating MAOC concentrations and deficits for soils with a wide range of physicochemical properties.

Fruit production in the Okanagan Valley of British Columbia is dominated by apple, sweet cherry, and wine grape. The relative importance of sweet cherry and grape has increased in recent decades, but little was known of the plant-parasitic nematodes associated with those crops. Soil samples analyzed for plant-parasitic nematodes were collected from a total of 39 apple orchards, 61 cherry orchards, and 57 vineyards; most were collected in 2018, but 36 cherry orchards were sampled in 2012. Soil properties were also assessed and related to nematode population densities. Nematode genera of potential significance were, in order of prevalence, Pratylenchus, Mesocriconema, Xiphinema, Paratylenchus, Paratrichodorus, Hemicycliophora, and Meloidogyne. Pratylenchus were found in 79, 98, and 81% of the apple, cherry, and grape plantings, respectively; Mesocriconema were found in 51, 79, and 82%; and Xiphinema were found in 59, 51, and 77%. Population densities of the three dominant genera were influenced more by soil texture than any other soil characteristics, with Pratylenchus being negatively correlated with percentage clay, Mesocriconema positively correlated with percentage sand, and Xiphinema positively correlated with percentage silt. The high prevalence of Mesocriconema in cherry orchards and vineyards in this region is significant because Mesocriconema is known to be an important pest of other Prunus crop species and grapevines in other regions. This study therefore provides a rationale for increasing grower awareness and research efforts on the impacts and management of Mesocriconema and other plant-parasitic nematodes in orchards and vineyards in the region.

Agricultural practices such as annual crop production, land use change and grazing on marginal lands lead to a loss of soil carbon (C) stock. But soil C losses are not universal in agricultural systems and modest soil C gains can occur when constraints such as a lack of water are removed. To characterize this we used a meta-analysis of published data focused on semi-arid regions, where irrigation is required for crop production. We showed that soil C stocks declined under cereals, cotton, maize and non-woody horticultural crops when compared to native unirrigated adjacent grassland or shrubland. By contrast, cultivation of irrigated, woody perennial crops generally leads to an accumulation of soil C. Identifying the mechanisms by which C is retained in the soils beneath woody perennial crops, and any limits to C accumulation, was the main goal of this study. A mechanistic understanding of soil organic C content accumulation, upon land use change, can be gained by dividing soil into particulate organic matter (POM) and mineral associated organic matter (MAOM). Here, we analyzed the C and natural abundance C-13 concentrations in POM and MAOM fractions in soils from eight apple orchards and eight vineyards irrigated using a dripline, and eight apple and eight cherry orchards irrigated with micro-spray. Samples were also taken from eight native grassland areas adjacent to the agricultural sites for comparison. Several decades of woody crop production doubled the average soil C concentration in comparison to the native sites, from to 10.1 +/- 1.48 g C kg(-1) to 20.1 +/- 0.96 g C kg(-1) over a depth of 0-15 cm. Most of the C was associated with POM, which increased in concentration from 7.9 +/- 1.19 g C kg(-1) to 14.2 +/- 0.79 g C kg(-1) in 0-15 cm soils, an increase of 80%. This was crop dependent, being highest in the cherry orchards and lowest in the vineyard soils. Although holding less C, the MAOM concentration increased by 166%, changing from 2.22 +/- 0.33 to 5.91 +/- 0.62 g C kg(-1); no differences existed between crops but the MAOM C concentration appeared to be constrained to a maximum value of similar to 12 g C kg(-1). MAOM and POM had markedly different delta C-13 values: MAOM was more enriched, indicative of greater microbial processing, whereas POM had a lower delta C-13 value consistent with the dominant standing vegetation. delta C-13 values were more depleted in both fractions at the agricultural sites compared to the native sites, indicating the accumulation of greater amounts of less processed C at the agricultural sites, due to higher C inputs. We conclude the soils in this region respond to irrigated perennial woody crop production by retaining C within both POM and MAOM fractions. Accumulation of C as MAOM is constrained by the minerology of the soils in this region, but is unconstrained for POM which dominates the soil C content, and is potentially vulnerable to changes in management practices and land use.

Increasing the carbon (C) content of agricultural soils can help mitigate rising atmospheric CO2 concentrations, improve soil health and increase crop yield. Unlike annual cropping systems, soils planted to perennial woody crops, such as vineyards and orchards, are left undisturbed for many years making them particularly amenable to soil C storage. Here, we used a regional sampling campaign of over 80 commercially-managed sites across the Okanagan Valley, in the southern interior of British Columbia, Canada, to examine the spatial distribution of soil C under irrigated perennial woody crops. Using this living lab approach, we collected soils from the crop and drive rows of apple and cherry orchards, and vineyards subjected to a wide range of real-life management regimes (e.g., for weed and pest control, fertilizer application, etc.). Sites were selected with soils belonging to five surficial deposit classes, representing 40% of the mapped agricultural land area. Soil C was spatially heterogeneous across all the sites, with the surface soil (0-15 cm) of drive rows containing more C than the soil in adjacent crop rows. Clear differences emerged among cropping systems, despite the variation in management practices applied by individual growers. Drip-irrigated apple orchards showed the greatest spatial heterogeneity, with C concentrations of 2.9% in the drive row and 1.8% in the crop row, while vineyard and cherry orchard soils showed the least, with differences between crop and drive rows of approximately 0.3%. Higher C concentrations in the drive rows appeared to be the result of recently assimilated/less processed litter and fine root C inputs from the shallow-rooted understory vegetation. This was confirmed using stable isotope analysis: drive row soil C was significantly C-13 depleted compared to the crop row soil, to a depth of 30 cm. Overall, cherry orchards contained the most C (70 Mg C ha(-1) to a depth of 30 cm), vineyards the least (48 Mg C ha(-1)), and apple orchards were intermediate (66 Mg C ha(-1)). A recent land-use survey in 2015 determined that 8501 ha of agricultural land in the Okanagan Valley was planted to apples, cherries or grapes, and that large shifts in crop land area have occurred since the previous survey, conducted in 2006. We estimate that apple orchards currently hold approximately 199 Gg C, vineyards 188 Gg C and cherry orchards 110 Gg C. Marked differences in soil C storage between the cropping systems, despite the fact some were less than 10 years old, suggests that soils in this region are responsive to changes in crop and associated management practices over relatively short time periods. We conclude that the drive rows of vineyards offer the greatest scope for increased soil C storage among woody perennial horticultural cropping systems in the Okanagan Valley but that 'long-term' soil carbon storage may not be possible in these soils.

Increasing soil carbon stocks in agricultural grasslands has a strong potential to mitigate climate change. However, large uncertainties around the drivers of soil respiration hinder our ability to identify management practices that enhance soil carbon sequestration. In a context where more intense and prolonged droughts are predicted in many regions, it is critical to understand how different management practices will temper drought-induced carbon losses through soil respiration. In this study, we compared the impact of changing soil volumetric water content during a drought on soil respiration in permanent grasslands managed either as grazed by dairy cows or as a mowing regime. Across treatments, root biomass explained 43% of the variability in soil respiration (p < 0.0001). Moreover, analysis of the isotopic composition of CO2 emitted from the soil, roots, and root-free soil suggested that the autotrophic component largely dominated soil respiration. Soil respiration was positively correlated with soil water content (p = 0.03) only for the grazed treatment. Our results suggest that the effect of soil water content on soil respiration was attributable mainly to an effect on root and rhizosphere activity in the grazed treatment. We conclude that farm management practices can alter the relationship between soil respiration and soil water content.

Anthropogenic activities including metal contamination create well-known problems in coastal mangrove ecosystems but understanding and linking specific pollution sources to distinct trophic levels within these environments is challenging. This study evaluated anthropogenic impacts on two contrasting mangrove food webs, by using stable isotopes (δ13C, δ15N, 87Sr/86Sr, 206Pb/207Pb and 208Pb/207Pb) measured in sediments, mangrove trees (Rhizophora mangle, Laguncularia racemosa, Avicennia schaueriana), plankton, shrimps (Macrobranchium sp.), crabs (Aratus sp.), oysters (Crassostrea rhizophorae) and fish (Centropomus parallelus) from both areas. Strontium and Pb isotopes were also analysed in water and atmospheric particulate matter (PM). δ15N indicated that crab, shrimp and oyster are at intermediate levels within the local food web and fish, in this case C. parallelus, was confirmed at the highest trophic level. δ15N also indicates different anthropogenic pressures between both estuaries; Vitória Bay, close to intensive human activities, showed higher δ15N across the food web, apparently influenced by sewage. The ratio87Sr/86Sr showed the primary influence of marine water throughout the entire food web. Pb isotope ratios suggest that PM is primarily influenced by metallurgical activities, with some secondary influence on mangrove plants and crabs sampled in the area adjacent to the smelting works. To our knowledge, this is the first demonstration of the effect of anthropogenic pollution (probable sewage pollution) on the isotopic fingerprint of estuarine-mangrove systems located close to a city compared to less impacted estuarine mangroves. The influence of industrial metallurgical activity detected using Pb isotopic analysis of PM and mangrove plants close to such an impacted area is also notable and illustrates the value of isotopic analysis in tracing the impact and species affected by atmospheric pollution.

Understanding the processes that drive the release of carbon dioxide (CO2) from soil is essential to combat rising atmospheric greenhouse gases. Whilst significant research has focused on soil organic carbon (C) dynamics, soil inorganic C has received much less attention. In arid and semi-arid regions, crops are often irrigated with water containing inorganic (bicarbonate) C, which can be a source of CO2 emissions. CO2 released from dissolved bicarbonates is C-13 enriched compared to that from organic sources in the soil (e.g., organic matter and respiring roots). Measurement of delta(CO2)-C-13 at the soil surface can therefore be used to trace CO2 sources. Using on-line C-13 analysis, we monitored delta(CO2)-C-13 and rate of soil CO2 emissions in an apple orchard in British Columbia, Canada, irrigated with bicarbonate-containing irrigation water drawn from Okanagan Lake. In Experiment 1, we applied deionised or irrigation water to wet and dry soils; in Experiment 2, we applied irrigation water from Okanagan Lake to soils with and without a surface mulch. In both experiments, soil efflux responded within seconds to application of water. In Experiment 1, a 6 parts per thousand enrichment of (CO2)-C-13 followed the application of irrigation water, confirming the contribution of bicarbonate-C to soil surface efflux, whereas a 4 parts per thousand depletion of (CO2)-C-13 followed the application of deionised water, suggesting a stimulation of labile organic C mineralisation. Experiment 2 confirmed that bicarbonates in irrigation water contribute to soil CO2 efflux; surface mulch had no effect on the response of CO2 release following irrigation. Using an isotopic mass balance model, we calculated that bicarbonates dissolved in irrigation water accounted for between 9 and 15% of total soil surface efflux, and estimate that irrigation with Okanagan Lake water generates on average > 45,000 kg bicarbonate-derived CO2 each year.

The extended National Waters Inventory of Scotland (NWIS) monitoring network in combination with an extensive, supplementary low flow sampling campaign was used to create isoscapes of surface water for management purposes at high spatial resolution (100 m grid) across Scotland. The 8 2 H isoscape shows a strong isotopic separation along a north-south and east-west topographic (mountainous to the north and west and lowlands to the east) and climatic (wetter west, drier east) gradients. Isotopes were enriched in the western domain and depleted in the east and central Highland domains. The surface water d-excess isoscape show more complex spatial variability mainly related to contrasting moisture sources (sub-tropical North Atlantic Ocean, the North Sea, Polar Continental, and the Arctic) as well as secondary evaporation processes. The two-year NWIS isotope record exhibited a significant seasonal evaporative effect on surface water isotopes that progresses from winter through to a maximum in autumn as indicated by Local Evaporation Lines (LELs). The surface water isoscapes can be efficiently reproduced with geographically weighted regression (GWR) models using gridded annual precipitation, remotely sensed actual evapotranspiration, land cover, soil wetness, catchment area, and mean elevation. The GWR models showed potential to assess isotopic changes under future climate and land use change.

In many forest ecosystems, plant-available pools of Mg, Ca, and K are assumed to be stored in the soil as exchangeable cations adsorbed on the cation exchange complex (exchangeable pools). However, between soil minerals and exchangeable cations exists a gradient of Mg, Ca, and K storage forms that have not been fully characterized and may play an important role in plant nutrition and biogeochemical cycles. We hypothesize that sources of Mg, Ca, and K in the soil other than the conventionally measured exchangeable pools are plant-available on very short time scales (<1 day). In the present study, we developed and applied an isotopic dilution technique using the stable isotopes (26)mg, Ca-44, and K-41 to trace and quantify the pools of Mg, Ca, and K (isotopically exchangeable pools) in the soil of a hardwood forest that contribute directly to equilibrium processes between the soil water and the soil. We characterize the equilibrium between the soil and soil solution using both a batch approach and a flow-through approach in order (i) to develop and determine the best routine method to measure the isotopically exchangeable pools and (ii) to further the characterization of the forms of storage of Mg, Ca, and K in the isotopically exchangeable pools. We first show that the flow-through reactor approach (equilibrium in unsaturated soil columns) is the most adequate to measure the isotopically exchangeable pools with the fewest equilibrium disturbances. We then show that isotopically exchangeable pools of Mg, Ca, and K are greater than traditionally measured exchangeable pools. The isotopically exchangeable pools of Mg, Ca, and K are mainly composed of traditionally measured exchangeable pools (88.8-98.5% for Mg, 74.7-97.7% for Ca, and 68.7-77.1% for K) but are also composed of pools extracted with the Tamm reagent (oxalic acid, pH 3) and nitric acid (1 mol.L-1): 1.5-11.2% for Mg, 2.3-25.3% for Ca, and 22.9-31.3% for K. Storage forms of Mg, Ca, and K in the isotopically exchangeable pool could include chelation with soil organic matter, retention on soil aluminum and iron oxides and hydroxides through phosphate and/or organic acid bridges and site-specific adsorption. The isotopic dilution method is a relevant tool to quantify the plant-available pools of Mg, Ca, and K on short time scales (source and sink pools) and is a very promising approach to characterize and quantify the processes responsible for the depletion and/or replenishment of these pools over longer time scales.

Soils can be sources or sinks of carbon depending on the balance between carbon inputs from plants and losses from the decomposition of soil organic matter (SOM). A good understanding of the temperature sensitivity of SOM decomposition is critical for forecasting whether soils in a warming world will lose or gain carbon, and therefore accelerate or mitigate the rate of increasing atmospheric carbon dioxide (CO2) concentration. We provide new evidence to show that the response of SOM decomposition to temperature may be constrained by substrate availability to microbial decomposers. We used laboratory incubations of a grassland soil to compare the temperature sensitivity of SOM decomposition with unmodified substrate availability with that of the same soil in which substrate availability was reduced by adding allophone, a clay-size mineral with a high capacity for binding SOM. In the soil with no added allophone, the decomposition rate increased about 7-fold over the temperature range from 1 to 40 degrees C. With added allophone, decomposition rate increased only about 3 fold over the same temperature range. We then used a non-disruptive, natural abundance isotopic technique at our field site to partition total soil respiration into CO2 efflux from newly released, C-13-depleted SOM (root respiration and rhizosphere decomposition) from CO2 efflux from older C-13-enriched SOM from the decomposition of more stable SOM. We found no increase in the decomposition rate of the C-13-enriched pool of SOM between 11 and 28 degrees C. That finding contrasts with most previous studies that have generally reported strong increases in SOM decomposition with temperature. We hypothesised that the large temperature sensitivity observed in laboratory incubations was due to substrate becoming readily available as a result of the disturbance involved in collecting soil samples. In undisturbed field conditions, the limiting step for the decomposition of the more stable SOM pool may be the rate at which decomposable substrate becomes available for decomposition. Our findings will have important implications for the feedbacks between soil carbon storage and the rate of increase in atmospheric CO2 concentration mediated by global warming.

Laboratory studies have shown that priming effects, caused by inputs of carbon into the rhizosphere, can change the rate of soil organic matter (SOM) decomposition and could have significant impacts on soil carbon cycling. However, there have been few studies in field conditions because of experimental constraints but field data are needed to improve models that forecast the effects of climate change on SOM decomposition rates and the impact of these changing rates on atmospheric CO2 concentration. In 2009 a fire at a Eucalyptus forest site in Australia killed all standing vegetation. Trenched plots were installed in 2010, approximately 12 months after the fire, and were maintained plant-free for the subsequent year. In 2011, after forest re-growth outside the trenched plots, we compared SOM decomposition rates in the presence of plants (rooted plots) and in the absence of plants (trenched plots) using a natural abundance stable carbon isotope technique with minimal disturbance of the soil. We then compared our results to those obtained in another study conducted at the same time and the same plots using laboratory incubations of sieved soil samples. There was no difference in SOM decomposition rates between the trenched and the rooted plots estimated using our non-disruptive technique. In contrast, laboratory incubations of sieved soils highlighted a two-fold increase in SOM decomposition rates in the rooted plots compared with rates from the trenched plots. Our results suggest that rhizosphere priming may not actively influence soil carbon turnover in the undisturbed soil environment and question conclusions from laboratory incubation studies. We attribute the different findings from laboratory and field studies to the physical disturbance of the soil involved in laboratory incubations causing the release of previously protected substrates, making them available for decomposition.

The carbon (C) sequestration potential of land-use practices is increasingly important. Trees sequester atmospheric C into biomass and above and belowground litter but may also prime the decomposition of soil organic matter (SOM). We compared the influence of Acer pseudoplatanus (Sycamore) and Larix x. europlepsis (Hybrid Larch) on soil C decomposition.

Applications of nitrogen to vineyard foliage or soil at veraison can improve grape juice yeast assimilable nitrogen concentrations and may prevent the excessive vine growth, delayed maturity, and adverse changes in fruit properties sometimes associated with high applications of N earlier in the growing season. However, the consequences of late-season foliar- and soil-applied nitrogen for grape juice yeast assimilable nitrogen (YAN) and, specifically, grape juice amino acid profiles have rarely been directly compared. Over two years in drip-irrigated Merlot and Pinot gris vineyards, grape juice amino acid concentrations were measured from vines to which urea had been applied three times around veraison at 3.8 g N/vine to either the foliage or the soil surface. Foliar-applied urea (applied as a 2% w/v solution) was usually more effective at boosting grape juice ammonium and amino acid concentrations, although soil-applied urea improved some grape juice amino acids at the Pinot gris site. Changes in the amino acid profiles of grape juice, observed in response to foliar N applications but not soil N applications, may have implications for wine quality. Applications of 15N-labeled urea at the Pinot gris site demonstrated that a greater percentage of fertilizer N was incorporated into grape juice amino acids when urea was applied to the foliage than when it was applied to the soil surface. Late-season foliar applications of urea are a reliable, efficient, and effective method of improving grape juice YAN. Further work is required to examine how treatment effects vary among sites and cultivars under different management practices and to understand the implications of altered grape juice amino acid profiles for wine quality.

Irrigated agriculture is conducted on approximately 257 million hectares worldwide and continues to expand, particularly in arid to semi-arid regions. Applications of water containing dissolved calcium and bicarbonate ions cause the precipitation of calcium carbonate in the soil and the release of carbon dioxide into the air. However, the contribution of inorganic C to CO2 emissions from the soil is rarely considered. Using a short-term incubation technique developed to examine changes in mineralizable organic C pools, we found that soils beneath drip emitters in an irrigated apple orchard released CO2 from both organic and inorganic C. Soils under drippers had higher concentrations of carbonates than soils that had not received direct inputs of irrigation water. The quantity of carbonates detected in the soil under the drippers at this site was small but may be greater on sites using irrigation water with higher concentrations of Ca2+ and HCO3−. Furthermore, site productivity may be reduced by unfavourable physical and chemical changes caused by carbonate deposition within the small soil volume occupied by tree roots in micro-irrigated orchards with dwarfing rootstocks. In order to better understand the implications for site productivity and for global C flux of carbonate precipitation in micro-irrigated systems, future work is required to quantify CO2 emissions during irrigation, and to characterize soil chemical and physical properties through the soil profile.

Root-respired δ13CO2 can be useful for exploring plant carbon allocation and root respiratory fractionation as well as for partitioning soil-surface CO2 emissions into plant root and soil organic matter (SOM) sources, a necessary measure for calculating the contribution of heterotrophic respiration of soil carbon to net ecosystem exchange. Root CO2 is usually sampled from excised roots, however, excision alters respiration rate and isolates the root sample from aboveground plant processes.

Summary The land use and climate of Scotland are currently undergoing change. Concentrations of Natural abundance stable isotopes in ecosystems have been used extensively to help to understand a wide range of processes and functions. In the current study topsoil was collected from the intercepts of a 20‐km grid across the whole of Scotland (183 points), which encompass large differences in mean annual temperature ( MAT ,3.1–9.1°C), mean annual precipitation ( MAP , 588–3470 mm) and land use (from arable land through grassland and woodland to less fertile moorlands and bogs). At each sampling point the natural abundance δ 13 C and δ 15 N values were measured. This paper describes for the first time the spatial distribution of these isotopes in the topsoil of Scotland. We applied linear modelling to assess the extent to which land use and climate can control the observed distributions. The more enriched topsoil δ 13 C values occurred in the northern and western regions of Scotland. Topsoil δ 13 C values were tightly constrained about the mean, and possibly because of this we were able to explain only 23.6% of the variance even after considering the potential effects of a wide range of abiotic factors and land uses. Precipitation and land use explained the greatest variance in topsoil δ 13 C , but individually this was only 10.4 and 9.9%, respectively. Topsoil δ 15 N values showed a more complex spatial arrangement. The main areas of the more enriched δ 15 N values were in the northern isles, along or near the coast on the eastern side of the country and in some areas of the western mainland. For topsoil δ 15 N , all explanatory variables together explained 55.7% of the variance, with land use alone explaining 45.4%. Soil under arable land and improved grassland, the more fertile sites, had the most enriched δ 15 N values, whereas woodland and bogs had the most depleted values. A positive relationship between topsoil δ 15 N and potential rate of nitrification suggested that this was due, at least in part, to greater losses of nitrate under arable land and improved grassland.

RATIONALEMicrobial degradation of soil organic matter (heterotrophic respiration) is a key determinant of net ecosystem exchange of carbon, but it is difficult to measure because the CO2 efflux from the soil surface is derived not only from heterotrophic respiration, but also from plant root and rhizosphere respiration (autotrophic). Partitioning total CO2 efflux can be achieved using the different natural abundance stable isotope ratios (δ13C) of root and soil CO2. Successful partitioning requires very accurate measurements of total soil efflux δ13CO2 and the δ13CO2 of the autotrophic and heterotrophic sources, which typically differ by just 2–8 ‰.METHODSIn Scottish moorland and grass mesocosm studies we systematically tested some of the most commonly used techniques in order to identify and minimise methodological errors. Typical partitioning methods are to sample the total soil‐surface CO2 efflux using a chamber, then to sample CO2 from incubated soil‐free roots and root‐free soil. We investigated the effect of collar depth on chamber measurements of surface efflux δ13CO2 and the effect of incubation time on estimates of end‐member δ13CO2.RESULTS(1) a 5 cm increase in collar depth affects the measurement of surface efflux δ13CO2 by –1.5 ‰ and there are fundamental inconsistencies between modelled and measured biases; (2) the heterotrophic δ13CO2 changes by up to −4 ‰ within minutes of sampling; we recommend using regression to estimate the in situ δ13CO2 values; (3) autotrophic δ13CO2 measurements are reliable if root CO2 is sampled within an hour of excavation; (4) correction factors should be used to account for instrument drift of up to 3 ‰ and concentration‐dependent non‐linearity of CRDS (cavity ringdown spectroscopy) analysis.CONCLUSIONSMethodological biases can lead to large inaccuracies in partitioning estimates. The utility of stable isotope partitioning of soil CO2 efflux will be enhanced by consensus on the optimum measurement protocols and by minimising disturbance, particularly during chamber measurements. Copyright © 2014 John Wiley & Sons, Ltd.