Study area

This study was carried out in North Selangor Peat Swamp Forest (NSPSF), Malaysia, an ombrotrophic peatlands, which contains large areas of forest cover and high water tables19. The area of NSPSF is 73,600 ha, the site is split into two separate management areas: The northern part form the 50,100 ha Sungai Karang Forest Reserve while the southern parts is in the 23,500 ha Raja Musa Forest Reserve39. The area has a history as state land which resulted in logging and deforestation of part of the peatland. Logging was much reduced after 1990 when the area was designated as a reserve40. The logging history of the area means that the condition of the forest varies considerably. Furthermore, the forest is traversed by a network of ca 500 km of narrow canals that previously were used for transporting timber. Some areas of the reserve still has good quality dense forest as they have not been logged for ca. 40 years and these were selected as the forest sites used for this study41. The forest is largely comprised by the following tree species: Macaranga pruinosa, Campnospermacoriaceum, Blumeodendron tokbrai, Shorea platycarpa, Parartocarpus venenosus, Ixora grandiflora, Pternandra galeata, Crytostachys sp., and Pandanus atrocarpus42.

The site first became forested during the early Holocene when it was colonised by mangroves, these were over time replaced by fresh water vegetation and forest communities. At the base of the peatland are grey marine clays over which peat deposits has accumulated to up to 5 m depth42. The mean annual rainfall is more than 2000 mm per year, with a dry period in June, when rainfall is between 76 to 191 mm, the largest amount of rain falls in November when precipitation is 185 to 414 mm43. The mean annual air temperature is 28.5 °C and the humidity is 77.2%44. Although the majority of the reserve remains forested, it is encroached upon at the periphery by oil palm plantations at both early and mature stages45. As part of the study we chose four land use types that represent the stages of conversion from peat swamp forest to oil palm plantation, namely: (1) secondary ‘forest’ – these sites were located in areas with low recent anthropogenic impact, though the whole forest reserve was selectively logged during the 20th century; (2) recently ‘drained’ but not cleared forest—at these sites, drainage took place ca. 6 months prior to sampling, drainage ditches were ca. 2 metres deep and 200–300 m apart; (3) drained, cleared and recently planted ‘young oil palm’ plantation which was established ca. six months prior to sampling—at the time of sampling the oil palms were 0.5 to 1 m tall; and (4) ‘mature oil palm’ first generation plantations, which were 10–15 years old with most trees between 8 and 12 m in height (see Tonks et al.19 and Table 1 for details).

Field sampling and laboratory analysis

Within each of these four land use types, five sites were selected. At each site, a 30 by 30 m plot was established, the location of each plot was determined using random coordinates. Within the plot, three replicate static head space chambers of known volume (11.5 dm3) and area (425 cm2) were inserted to 2 cm depth and used to sample CO 2 , CH 4 and N 2 O21 through a Suba seal; thus there were 60 sampling locations for each sampling event. At the young and mature oil palm plantations (stages 3 and 4), samples were collected 3.5 m away from the palm trunk to ensure negligible contribution of autotrophic respiration to measured surface CO 2 fluxes6,7,32. During soil sampling and chamber installation, observations of ca. 10 cm diameter soil samples collected at 0–10 cm depth and ca. 5 cm diameter soil samples collected from 40–50 cm depth from each plot confirmed that there were no oil palm roots at the sampling locations. This was not possible at the forest sites; instead we applied a 63.2% contribution of autotrophic respiration to correct the surface fluxes at the secondary and drained forest sites24,46. Very similar rates of autotrophic respiration have been reported from peat swamp forest in SE Asia and the Neotropics24,46. Gas sampling was repeated three times at the forest, young oil palm and mature oil palm sites during the 2014 wet season (October-December); repeat sampling was not possible at the drained sites due to access problems. The overall sampling programme resulted in 150 independent sampling points across the 20 different sites. Samples were collected at 0, 2, 6 and 10 min using hypodermic needles and 20 ml syringes (25 G × 1”, TERMO, UK). The air within the chambers was gently mixed prior to sample extraction using the syringe and needle. Samples were then injected into pre-evacuated 12 ml glass vials (Exetainers, Labco, UK). All samples were shipped to the University of Nottingham, UK for gas chromatography analyses.

Vials were discarded for chromatographic analyses if overpressure was absent (<5 out of a total of 600 vials). CO 2 , CH 4 and N 2 O concentrations were determined using a single injection system with a 1 mL sample loop that passed the gas sample using N 2 as carrier through a non-polar methyl silicone capillary column (CBP1-W12-100, 0.53 mm I.D., 12 m, 5 mm; Shimadzu UK LTD, Milton Keynes, UK) and porous polymer packed column (HayeSep Q 80/100). Thermal conductivity (TCD), flame ionisation (FID) and electron capture (ECD) detectors were used to measure CO 2 , CH 4 and N 2 O concentrations, respectively. Flux calculations were made using the ideal gas law and all samples were checked that gas accumulation in the head spaces were linear over time.

Drainage and lowered water tables are key features of conversion of peat swamp forest to oil palm plantation and can affect GHG production strongly5. Therefore, water table depth was measured at the time of GHG sampling at each field plot using dip wells. To explore longer term variation in water table depth, monthly variation was measured over a two-year period using dipwells at two locations in the secondary forest.

Structural woody vegetation measurements were taken at the field plots. At the forest and drained sites, diameter at breast height (DBH; calculated via circumference measured at a height of 140 cm) was calculated for all trees with DBH > 10 cm. From these data, basal area and stem density per ha were calculated. At young oil palm and mature oil palm sites, trunk height of all trees was estimated using a clinometer and tape measure.

Surface peat samples (10×10×10 cm volume) were collected using a bread knife at the first sampling event adjacent to the gas sampling locations in each of the field plots. Samples were placed in plastic bags and shipped to the University of Nottingham, UK. Prior to analysis, samples were cold stored at 4°C. Surface peat pH was determined by mixing 5 cm3 of field-wet peat in 12.5 cm3 of distilled water in centrifuge tubes and leaving on a rotary shaker overnight, before measuring with a pH 209 benchtop pH metre (Hanna Instruments Ltd.) and combination pH electrode.

Gravimetric water content was assessed by oven drying the peat samples at 105 °C for 48 h. The peat mass was recorded before and after oven drying and applied to Eq. (1). Bulk density was determined using the oven dried mass and known volumes, as in Eq. (2). Organic matter content was quantified using the loss on ignition method. 5 g samples of oven dried, ball milled peat were weighed into porcelain crucibles, before being placed in a Carbolite AAF muffle furnace (Carbolite Ltd.) at 550 °C for 4 h. The weight of ash left after ignition was recorded and Eq. (3) was used to determine the percentages of organic matter.

$$\theta = \frac{{M_{\mathrm{w}} - M_{\mathrm{d}}}}{{M_{\mathrm{d}}}} \times 100$$ (1)

Where θ is the gravimetric water content, dry weight basis (%); M w is the mass of wet peat (g); and M d is the mass of oven dry peat (g).

$$\rho _{{\mathrm{bulk}}} = \frac{{M_{\mathrm{d}}}}{V}$$ (2)

Where ρ bulk is the bulk density, dry weight basis (g cm−3); M d is the mass of oven dry peat (g); and V is the volume of the peat core (cm3).

$${\mathrm{OM}} = \frac{{M_1 - M_2}}{{M_1}} \times 100$$ (3)

Where OM is the organic matter content (%); M 1 is the mass of oven-dry peat (g); and M 2 is the mass of ash left after ignition (g).

Data analysis and calculation of emissions factors

Mixed models using residual maximum likelihood method (REML) were used to test for differences in GHG fluxes between land uses. Land use type and time were used as fixed effects, ‘plot’ was fitted as a random effect. The spatial subsamples within each site were averaged at each time point before statistical analysis. GHG flux data were assessed for normality and subsequently transformed logarithmically. Statistical analysis was conducted using Genstat (version 15.1.0). We used the means from the measuring period (November – December 2014) to estimate annual fluxes, calculating GWP (CO 2 equivalents) using equivalent values for CH 4 and N 2 O of 34 and 298, respectively47. To determine whether variation in the water table affected the measured fluxes, linear relationships between gas flux and water table position for each combination of GHG (CO 2 , CH 4 , N 2 O) and land use (forest, drained, young oil palm, mature oil palm) were tested. There were no significant relationships between short term site water table fluctuations and any of the three GHGs in line with findings by Carlson et al.48, hence the mean measured gas fluxes were used to calculate emissions factors across the year. Note that although measurements were made during the wet season, water tables range widely between sites and over time including in the mature oil palm plantations which were flooded at some sampling time points (Table 1).

To estimate a confidence interval on emissions factors for the converted system we undertook a monte carlo analysis in which the emission rates for each GHG and conversion stage were sampled from the appropriate observed log-normal distribution. To quantify the GHGs emissions over the full oil palm cycle of 30 years the time dependent emission rate was linearly interpolated between the sampled rates for each conversion stage. For this, we assumed that emission rates changed from the secondary forest to the drained forest value over a six month period and then to the young oil palm rate over a further six months. The period over which emission changes from the young oil palm stage to the more stable mature oil palm was allowed to vary using a triangular distributed value which varied from 4 to 6 years after initial conversion with the maximum at 5 years. While these assumptions simplify the influence of plantation age on emissions, they are in line with the observed year of the actual (forest drainage and clearance) conversion process, the account by Hooijer et al.15 of subsidence stabilisation after ca. 5–6 years of drainage, and the subsequently stable subsidence rates at 4.2 mm yr−1 for the rest of the oil palm plantation life cycle reported for peatlands in Peninsular Malaysia49. The assumptions of comparable decomposition rates between ca. 5–6 and 30 years since conversion is supported by the paper by Dariah et al.7 who found no significant differences in CO 2 emissions between 6 and 15 year old oil palm plantations, and the paper by Hooijer et al.31 which shows consistent subsidence rates after 6 years whereby subsidence indicates decomposition of peat. Indeed, Cooper et al.17 suggest rapid decomposition of labile carbon during the early stage of conversion followed by more gradual decomposition during the mature phase, supporting the notion of relatively consistent decomposition rates in the later stage of plantation when most of the labile carbon has already been metabolised by the microbial community and released to the atmosphere. Based on these assumptions, we calculated time integrated emissions factors (combining all three GHGs accounting for their contrasting GWP) for forest, drained, young oil palm and mature oil palm sites (Table 2).

Reporting summary

Further information on research design is available in the Nature Research Reporting Summary linked to this article.