Panchromatic modeling is one of the most powerful tools at our disposal to measure reliably the physical properties of galaxies across cosmic times. We present here an entirely new implementation in ...python of one such tool: CIGALE. Developed along three main design principles: simplicity, modularity, and efficiency, it has proven to be a versatile code that in addition to estimating the physical properties of galaxies (or regions within galaxies), can generate arbitrary sets of theoretical models or be used as a library to build other tools. Among its defining features, it is a truly panchromatic code ranging from the far-ultraviolet to the radio that takes into account numerous physical components (including active nuclei or synchrotron emission), that can fit non-photometric data, handle upper limits, determine photometric redshifts, and even build mock catalogs.
Selective logging is among the main causes of tropical forest degradation, but little is known about its effects on greenhouse gas (GHG) fluxes from highly weathered Ferralsol soils in Africa. We ...measured soil CO₂, N₂O, and CH₄ fluxes, and their soil controlling factors at two forests that had undergone conventional selective logging and reducedimpact logging in Cameroon. Each logging system had four replicate plots, each included the disturbed strata (road, logging deck, skidding trail, and felling gap) and an undisturbed reference area. Measurements were conducted monthly from September 2016 to October 2017. Annual GHG fluxes ranged from 4.9 to 18.6 Mg CO₂–C, from 1.5 to 79 kg N₂O–N, and from – 4.3 to 71.1 kg CH₄–C ha⁻¹ year⁻¹. Compared to undisturbed areas, soil CO₂ emissions were reduced and soil CH₄ emissions increased in skidding trails, logging decks and roads (P < 0.01) whereas soil N₂O emissions increased in skidding trails (P = 0.03–0.05). The combined disturbed strata had 28% decrease in soil CO₂ emissions, 83% increase in soil N₂O emissions, and seven times higher soil CH₄ emissions compared to undisturbed area (P B 0.01). However, the disturbed strata represented only 4–5% of the area impacted in both logging systems, which reduced considerably the changes in soil GHG fluxes at the landscape level. Across all strata, soil GHG fluxes were regulated by soil bulk density and waterfilled pore space, indicating the influence of soil aeration and gas diffusion, and by soil organic carbon and nitrogen, suggesting the control of substrate availability on microbial processes of these GHG.
In tropical forests, multi-year studies on the impact of chronic nitrogen (N) enrichment on soil N-oxide fluxes are lacking. Our objectives were to: (1) assess the changes in soil N-oxide (NO+N₂O) ...fluxes from a montane forest in response to 3–4 years of N addition and compare these to the response of a lowland forest with 11–12 years of N addition, (2) quantify the contributions of nitrification and denitrification to nitrous oxide (N₂O) emissions, and (3) assess how deep in the soil profile the N₂O concentrations are affected by N input. These measurements were conducted in montane and lowland forests in Panama in 2008–2009, which covered the last 2 years of a 4-year investigation that started in 2006. Each forest had a control and N addition treatment (125 kg urea N ha⁻¹ year⁻¹) with four replicate plots (1,600 m² each) per treatment. N-oxide emissions from the montane forest started to increase within the first 2 years of treatment and continued to increase in the 3rd and 4th years of N addition, during which the emissions were already equivalent to those from the lowland forest with 11–12 years of N addition. The large N-oxide response of the montane forest to N addition were due to the large increases in gross nitrification rates in the organic layer and the high moisture contents of the mineral soil due to the high rainfall (5.5 ± 0.2 m year⁻¹). In the lowland forest (2.7 ± 0.1 m rain year⁻¹), N-oxide response to N addition was more pronounced in wet years (i.e. 2006–2007 with 5–17 % higher rainfall than average) than in dry years (i.e. 2008–2009 with 5–26 % lower rainfall than average). Denitrification was the dominant source of N₂O not only for the organic layer and the top 5 cm of mineral soil but possibly also for the entire 2 m depth. Soil–air N₂O concentrations were elevated by N addition down to at least 2 m. Our results suggest that the best indicators of these responses were the presence of an organic layer and rainfall quantity and seasonality.
Although often overlooked in forest research, the canopy can play an important role in forest nutrient cycling. Since the canopy is spatially isolated from the forest floor, nutrient cycling in the ...two areas may differ as terrestrial nutrients accumulate. We measured rates of free-living N₂fixation along an elevation gradient (1,000, 2,000 and 3,000 m) of tropical montane canopy soils, compared these to rates measured in the top 5 cm of forest floor soils (excluding fresh litter), and assessed the effects of elevated nutrient inputs to the forest floor. N₂fixation was measured using the acetylene reduction assay. Measurements occurred in the field, in the wet and dry seasons, using intact cores of soil. The forest floor had been fertilized biannually with moderate amounts of nitrogen (N) and phosphorus (P) for 4 years; treatments included control, N, P and N + P. N₂fixation rates exhibited little variation with elevation but were higher in the dry season than the wet season. Fixation was inhibited in forest floor N plots compared to control and P plots, and stimulated in canopy P plots compared to control. At 2,000 m, the canopy contributed 12 % of measured canopy and forest floor N₂fixation (1.2 kg N ha⁻¹ year⁻¹). Results suggest that N₂fixation is an active process in canopy soils, which is variable across seasons and sensitive to changes in terrestrial nutrient availability. Long-term terrestrial accumulation of N and/or P has the potential to significantly change the dynamics of soil N cycling in these canopies.
Presently, the lack of data on soil organic carbon (SOC) stocks in relation to land-use types and biophysical characteristics prevents reliable estimates of ecosystem carbon stocks in montane ...landscapes of mainland SE Asia. Our study, conducted in a 10 000 ha landscape in Xishuangbanna, SW China, aimed at assessing the spatial variability in SOC concentrations and stocks, as well as the relationships of SOC with land-use types, soil properties, vegetation characteristics and topographical attributes at three spatial scales: (1) land-use types within a landscape (10 000 ha), (2) sampling plots (1 ha) nested within land-use types (plot distances ranging between 0.5 and 12 km), and (3) subplots (10 m radius) nested within sampling plots. We sampled 27 one-hectare plots – 10 plots in mature forests, 11 plots in regenerating or highly disturbed forests, and 6 plots in open land including tea plantations and grasslands. We used a sampling design with a hierarchical structure. The landscape was first classified according to land-use types. Within each land-use type, sampling plots were randomly selected, and within each plot we sampled within nine subplots. SOC concentrations and stocks did not differ significantly across the four land-use types. However, within the open-land category, SOC concentrations and stocks in grasslands were higher than in tea plantations (P < 0.01 for 0–0.15 m, P = 0.05 for 0.15–0.30 m, P = 0.06 for 0–0.9 m depth). The SOC stocks to a depth of 0.9 m were 177.6 ± 19.6 (SE) Mg C ha−1 in tea plantations, 199.5 ± 14.8 Mg C ha−1 in regenerating or highly disturbed forests, 228.6 ± 19.7 Mg C ha−1 in mature forests, and 236.2 ± 13.7 Mg C ha−1 in grasslands. In this montane landscape, variability within plots accounted for more than 50 % of the overall variance in SOC stocks to a depth of 0.9 m and the topsoil SOC concentrations. The relationships of SOC concentrations and stocks with land-use types, soil properties, vegetation characteristics, and topographical attributes varied across spatial scales. Variability in SOC within plots was determined by litter layer carbon stocks (P < 0.01 for 0–0.15 m and P = 0.03 for 0.15–0.30 and 0–0.9 m depth) and slope (P ≤ 0.01 for 0–0.15, 0.15–0.30, and 0–0.9 m depth) in open land, and by litter layer carbon stocks (P < 0.001 for 0–0.15, 0.15–0.30 and 0–0.9 m depth) and tree basal area (P < 0.001 for 0–0.15 m and P = 0.01 for 0–0.9 m depth) in forests. Variability in SOC among plots in open land was related to the differences in SOC concentrations and stocks between grasslands and tea plantations. In forests, the variability in SOC among plots was associated with elevation (P < 0.01 for 0–0.15 m and P = 0.09 for 0–0.9 m depth). The scale-dependent relationships between SOC and its controlling factors demonstrate that studies that aim to investigate the land-use effects on SOC need an appropriate sampling design reflecting the controlling factors of SOC so that land-use effects will not be masked by the variability between and within sampling plots.
Multiplex digital PCR (dPCR) enables noninvasive and sensitive detection of circulating tumor DNA with performance unachievable by current molecular-detection approaches. Furthermore, picodroplet ...dPCR facilitates simultaneous screening for multiple mutations from the same sample.
We investigated the utility of multiplex dPCR to screen for the 7 most common mutations in codons 12 and 13 of the KRAS (Kirsten rat sarcoma viral oncogene homolog) oncogene from plasma samples of patients with metastatic colorectal cancer. Fifty plasma samples were tested from patients for whom the primary tumor biopsy tissue DNA had been characterized by quantitative PCR.
Tumor characterization revealed that 19 patient tumors had KRAS mutations. Multiplex dPCR analysis of the plasma DNA prepared from these samples identified 14 samples that matched the mutation identified in the tumor, 1 sample contained a different KRAS mutation, and 4 samples had no detectable mutation. Among the tumor samples that were wild type for KRAS, 2 KRAS mutations were identified in the corresponding plasma samples. Duplex dPCR (i.e., wild-type and single-mutation assay) was also used to analyze plasma samples from patients with KRAS-mutated tumors and 5 samples expected to contain the BRAF (v-raf murine sarcoma viral oncogene homolog B) V600E mutation. The results for the duplex analysis matched those for the multiplex analysis for KRAS-mutated samples and, owing to its higher sensitivity, enabled detection of 2 additional samples with low levels of KRAS-mutated DNA. All 5 samples with BRAF mutations were detected.
This work demonstrates the clinical utility of multiplex dPCR to screen for multiple mutations simultaneously with a sensitivity sufficient to detect mutations in circulating DNA obtained by noninvasive blood collection.
Measurements of N transformation rates in tropical forest soils are commonly conducted in the laboratory from disturbed or intact soil cores. On four sites with Andisol soils under old-growth forests ...of Panama and Ecuador, we compared N transformation rates measured from laboratory incubation (at soil temperatures of the sites) of intact soil cores after a period of cold storage (at 5
°C) with measurements conducted in situ. Laboratory measurements from stored soil cores showed lower gross N mineralization and NH
4
+ consumption rates and higher gross nitrification and NO
3
− immobilization rates than the in-situ measurements. We conclude that cold storage and laboratory incubation change the soils to such an extent that N cycling rates do not reflect field conditions. The only reliable way to measure N transformation rates of tropical forest soils is in-situ incubation and mineral N extraction in the field.
Abstract
The difficulty of measuring gross N
2
O production and consumption in soil impedes our ability to predict N
2
O dynamics across the soil-atmosphere interface. Our study aimed to disentangle ...these processes by comparing measurements from gas-flow soil core (GFSC) and
15
N
2
O pool dilution (
15
N
2
OPD) methods. GFSC directly measures soil N
2
O and N
2
fluxes, with their sum as the gross N
2
O production, whereas
15
N
2
OPD involves addition of
15
N
2
O into a chamber headspace and measuring its isotopic dilution over time. Measurements were conducted on intact soil cores from grassland, cropland, beech and pine forests. Across sites, gross N
2
O production and consumption measured by
15
N
2
OPD were only 10% and 6%, respectively, of those measured by GFSC. However,
15
N
2
OPD remains the only method that can be used under field conditions to measure atmospheric N
2
O uptake in soil. We propose to use different terminologies for the gross N
2
O fluxes that these two methods quantified. For
15
N
2
OPD, we suggest using ‘gross N
2
O emission and uptake’, which encompass gas exchange within the
15
N
2
O-labelled, soil air-filled pores. For GFSC, ‘gross N
2
O production and consumption’ can be used, which includes both N
2
O emitted into the soil air-filled pores and N
2
O directly consumed, forming N
2
, in soil anaerobic microsites.
In tropical regions, shifting from forests and traditional agroforestry to intensive plantations generates conflicts between human welfare (farmers’ demands and societal needs) and environmental ...protection. Achieving sustainability in this transformation will inevitably involve trade-offs between multiple ecological and socioeconomic functions. To address these trade-offs, our study used a new methodological approach allowing the identification of transformation scenarios, including theoretical landscape compositions that satisfy multiple ecological functions (i.e., structural complexity, microclimatic conditions, organic carbon in plant biomass, soil organic carbon and nutrient leaching losses), and farmers needs (i.e., labor and input requirements, total income to land, and return to land and labor) while accounting for the uncertain provision of these functions and having an actual potential for adoption by farmers. We combined a robust, multi-objective optimization approach with an iterative search algorithm allowing the identification of ecological and socioeconomic functions that best explain current land-use decisions. The model then optimized the theoretical land-use composition that satisfied multiple ecological and socioeconomic functions. Between these ends, we simulated transformation scenarios reflecting the transition from current land-use composition towards a normative multifunctional optimum. These transformation scenarios involve increasing the number of optimized socioeconomic or ecological functions, leading to higher functional richness (i.e., number of functions). We applied this method to smallholder farms in the Jambi Province, Indonesia, where traditional rubber agroforestry, rubber plantations, and oil palm plantations are the main land-use systems. Given the currently practiced land-use systems, our study revealed short-term returns to land as the principal factor in explaining current land-use decisions. Fostering an alternative composition that satisfies additional socioeconomic functions would require minor changes (“low-hanging fruits”). However, satisfying even a single ecological indicator (e.g., reduction of nutrient leaching losses) would demand substantial changes in the current land-use composition (“moonshot”). This would inevitably lead to a profit decline, underscoring the need for incentives if the societal goal is to establish multifunctional agricultural landscapes. With many oil palm plantations nearing the end of their production cycles in the Jambi province, there is a unique window of opportunity to transform agricultural landscapes.
•Current tropical regions, like Jambi (Indonesia), lack multifunctional landscapes.•New land-use allocation model for identifying multifunctional transformation scenarios.•Farmers’ decisions are most likely dominated by a few socioeconomic functions.•Compromise solutions satisfying ecological functions require major shifts in land use.•Economic incentives are required to promote multifunctional agricultural landscapes.
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