Comparison of chlorophyll fluorescence curves and texture analysis for automatic plant identification

With automatic plant identification methods, the amount of herbicides used in agriculture can be reduced when herbicides are sprayed only on weeds. In the present study, leaves of oat (Avena sativa) and dandelion (Taraxacum officinale, TAROF) were arranged so that there was overlap between the species, imaged with a pulse amplitude modulation fluorescence camera and photographed with a digital color camera. The fluorescence induction curves from each pixel were parameterized to obtain a set of features and from color photographs, texture features were calculated. A support vector algorithm that also performed feature selection was used for pattern recognition of both data sets. Fluorescence-based identification worked well with oat leaves, producing 92.2 % of correctly identified pixels, whereas the texture-based method often mis-identified the central vein of a TAROF leaf as oat, identifying correctly only 66.5 % of oat pixels. With TAROF that shows a clear dicot-type texture, the texture method was slightly better (96.4 % correctly identified pixels) than the fluorescence method (94.6 %). In fluorescence-based identification, the accuracy varied between entire TAROF leaves, probably reflecting the genetic variability of TAROF. The results suggest that the accuracy of identification could be improved by combining two identification methods.     

Seasonal acclimation of photosystem II in Pinus sylvestris. I. Estimating the rate constants of sustained thermal energy dissipation and photochemistry

Acclimation of the partitioning of absorbed light energy in Photosystem II (PSII) between photochemical and non-photochemical processes includes short-term adjustments that are rapidly reversed in the dark and seasonal acclimation processes that are unaffected by dark acclimation. Thus, by using dark-acclimated leaves to study the seasonal acclimation of PSII, the confounding effect of short-term adjustments is eliminated. The maximum quantum yield of photochemistry, estimated by chlorophyll fluorescence analysis as F(v)/F(m), where F(v) = (F(m) - F(o)), and F(m) and F(o) are maximum and minimum chlorophyll fluorescence, respectively, has been widely used to follow the seasonal acclimation of PSII, because it is measured in dark-acclimated leaves. Seasonal changes in F(v)/F(m) can be caused by adjustments in either the photochemical capacity in PSII, or the capacity of thermal dissipation in PSII, or both. However, there is a lack of chlorophyll fluorescence parameters that can distinguish between these processes. In this study, we introduce two new parameters: the rate constants of sustained thermal energy dissipation (k(NPQ)) and of photochemistry (k(P)). We estimated k(NPQ) and k(P) from dark-acclimated F(o) and F(m) measured during spring recovery of photosynthesis in Scots pine (Pinus sylvestris L.) trees. We suggest that k(NPQ) and k(P) be used to study the mechanisms underlying the observed seasonal acclimation in PSII, because these parameters provide quantitative data that complement and extend F(v)/F(m) measurements.     

Direct experimental evidence for the contribution of lime to CO2 release from managed peat soil

Liming is a common management practice used to achieve optimum pH for plant growth in agricultural soils. Addition of lime to the soil, however, may cause CO₂ release when the carbonates in lime dissolve in water. Although lime may thereby constitute a significant carbon source, especially under acidic soil conditions, experimental data on the CO₂ release are lacking so far. We conducted a split-plot experiment within a cut-away peatland cultivated with a bioenergy crop (reed canary grass, Phalaris arundinacea L.) with lime and fertilizer treatments to determine effects of lime on the CO₂ emissions from soil and to better understand mechanisms underlying liming effects. Carbon dioxide release was measured over two growing seasons in the field after liming, and complementary laboratory studies were conducted. To differentiate CO₂ derived from lime and biotic respiration the δ¹³C of CO₂ released was determined and the two-pool mixing model was applied. The results showed that lime may contribute significantly to CO₂ release from the soil. In the laboratory, more than 50% of CO₂ release was attributable to lime-carbonates during short-term incubation. Lime-derived CO₂ emissions were much lower in the field, and were only detected during the first (2–4) months after the application. However, a maximum of 12% of monthly CO₂ emissions from the cultivated peatland originated from the lime. Biotic respiration rates were similar in limed and unlimed soils, suggesting that higher pH did not, at least in the short-term, increase carbon losses from cultivated peat soils. Additional fertilization and acidification did not contribute to further CO₂ release from the lime. According to our first estimations about one sixth of the lime applied would be released as CO₂ from the managed peatland, with all lime-derived emissions occurring during the first year of application (equivalent to about 4.6% of the total annual CO₂ losses from the soil in the first year). This suggests that the mass-balance approach as proposed by the IPCC Tier 1 methodology, which assumes that all carbon in lime ends up as CO₂ in the atmosphere, overestimates the emissions from lime. Our study further shows that there is a great risk to overestimate heterotrophic microbial activity in limed soils by measuring the CO₂ release without separating abiotic and biotic CO₂ production.     

Macroinvertebrate-Inferred Stream-Water Acidity in North Eastern Finland Along a Sulphur Deposition Gradient

Recently developed weighted averaging (WA) models and widely used tolerance-limit approaches for inferring stream minimum pH from macroinvertebrates were tested in northeastern Finnish Lapland. Surface waters there are threatened by large sulphur emissions in the Russian Kola Peninsula. The modelled sulphur deposition increases from west to east approximately parallel to longitude. The effect of deposition on stream minimum pH was assessed by relating the macroinvertebrate-inferred stream minimum pH to longitude. In a test set of 17 streams, the minimum pH inferred from pooled invertebrate samples of three seasons by WA models showed a strong correlation (r = 0.67–0.72) with the minimum pH (range 6.3–7.1) observed during the spring snow-melt period. The relationship was slightly weaker (r = 0.59–0.69) using autumn samples only. The tolerance-limit approaches assigned the streams into the correct acidity class, but the inferred pH was not related to the observed minimum pH. This further demonstrates the superiority of the WA approach, especially in detecting early signs of acidification. The minimum pH inferred by WA from autumn assemblages of 37 streams along the deposition gradient showed a significant negative correlation with longitude, suggesting that the emissions from the Kola region contribute to low pH events in streams of northeastern Finnish Lapland. The results demonstrate the potential of bioassessment and monitoring using invertebrates in detecting impacts and changes that could remain unnoticed by conventional water quality-analyses.     

Dimethyl sulphoxide (DMSO) and dimethyl sulphide (DMS) as inhibitors of methane oxidation in forest soil

Dimethyl sulphoxide (DMSO) at 14 mM inhibits CH₄ oxidation in forest soil, but the inhibition mechanism is unknown. When soil slurries are incubated in gas tight flasks, there is a lag of about 45 h before DMSO inhibits CH₄ oxidation. We tried to determine if some metabolic compound derived from DMSO, as a result of microbial activity, is responsible for the inhibition. Dimethyl sulphide (DMS) accumulated in the sealed flasks up to 5-83 μl l⁻¹ in the headspace during a 2-week period. DMS at 1 μl l⁻¹ in the headspace (0.64 μM in soil-water slurry) had a negligible effect on CH₄ oxidation but 50 μl l⁻¹ DMS (32 μM) inhibited CH₄ oxidation completely. However, the inhibition by DMSO was already evident after 45 h, when DMS concentrations were generally non-inhibiting (0.1-0.7 μl l⁻¹). DMSO was also shown to inhibit CH₄ oxidation when the DMS produced was continuously removed. Results suggest that the production of DMS from DMSO makes a minor contribution to the inhibition of CH₄ oxidation by DMSO with incubation times relevant in CH₄ oxidation studies.     

Growth and frost hardening of European aspen and backcross hybrid aspen as influenced by water and nitrogen

• Introduction  

The interactive effects of water and nitrogen (N) on frost hardiness are not well known in broad-leaved trees. Furthermore, new environmental conditions may favour naturally generated hybrids between native and introduced tree species over native species.     

Differentiating sources of CO2 from organic soil under bioenergy crop cultivation: A field-based approach using C

We tested here a plant-soil system to separate recent, plant-derived and native, soil-derived carbon in soil respiration. The approach uses a perennial crop cultivated on an organic soil where upper soil layers have been removed as a result of peat extraction. There, the ¹⁴C signal from native organic matter is highly depleted compared to that in vegetation established at the site after peat extraction ceased. Radiocarbon was analyzed in carbon dioxide respired from soil over one growing season, and a two-pool isotope mixing model was applied to calculate the relative contribution of old vs. new carbon sources. The analysis showed that the approach is reliable for source partitioning with isotopes. After six years of cultivation, old peat decomposition contributed less to total soil respiration than respiration of recent plant material (30% vs. 70% on average, respectively), but the relative proportions were highly variable over the growing season. The approach offers a new possibility to follow the fate of old, native soil organic matter in highly organic soils.     

Elevated temperature effects on germination and early growth of European aspen (Populus tremula), hybrid aspen (P. tremula × P. tremuloides) and their F2-hybrids

This study aimed to understand the interaction between temperature and genotype in terms of the effect on early seedling development of European aspen (Populus tremula) and various F₂-aspen hybrids. We evaluated the response of 16 different European aspen and F₂-hybrid families on seed germination, survival rate and seedling height in one- and two-family trials under three different temperature regimes. In one-family trials, higher germination and higher survival rates were observed in higher temperature (C1700), leading to taller seedlings. European aspen × hybrid aspen individuals (Asp × Hyb) had a higher survival rate and taller seedlings than Asp, Hyb × Asp or Hyb × Hyb individuals. The difference between Asp × Hyb and Hyb × Asp was pronounced. Both growth conditions and genotype (i.e., hybrid cross) had strong effects on germination, survival rate and height of European aspen and F₂-hybrid seedlings. However, the interaction of genotype and growth conditions also had a significant influence on survival rate and seedling height, but not on germination. Two-family trials involving European aspen and F₂-hybrids led to significant negative effects on germination and survival rate and also facilitation effects on seedling height. Similarly, genotype had strong effects on germination and survival rate. Different genotypes and traits affected survival rate and seedling height differently in different growth conditions. These differences were more pronounced in the warmest environment, i.e., 1,700 degree days. We conclude that introgression between F₂-hybrids and local European aspen is likely in the current climate, and any warming will likely favor certain F₂-hybrids, especially the most probable types (P. tremula × (P. tremula × P. tremuloides)).     

Increased atmospheric CO2 concentration enhances the development of photosynthetic capacity beyond the temperature effect for silver birch in simulated future climate

We conducted an experiment to find out how future climate conditions will impact the spring development of photosynthetic capacity of silver birch leaves. We had two greenhouse conditions. In the simulated future climate condition, we had both elevated temperatures and CO₂ concentration, while for reference we had trees growing under current climate conditions. We used two methods to measure the development of photosynthetic capacity: first, the maximum quantum efficiency of photosystem II with a fluorescence meter; and second, the CO₂ assimilation rate with gas exchange measurements. The development of full photosynthetic capacity took around two weeks following the bud burst. The maximum quantum efficiency developed slightly faster than the CO₂ assimilation rate. Both measurement methods showed that an elevated CO₂ concentration enhanced the development of photosynthetic capacity beyond the impact of temperature only. The enhancement under the conditions of our simulated climate change translates to achieving photosynthetic capacity up to five days earlier, which impact should be taken into account in simulations of photosynthetic productivity.     

Annual pattern of photosynthesis in Scots pine in the boreal zone

To detect seasonal changes in photosynthetic rate in the field, a set of 18,000 photosynthetic measurements made between April and October on three shoots of Scots pine growing near the northern timberline was studied. The measurements were analyzed in the framework of an optimal stomatal control model of photosynthesis, in which irradiance (photosynthetically active radiation, I), air humidity and ambient temperature are driving variables. All driving variables were monitored concomitantly with gas exchange measurements throughout the growing season. The model has nine parameters, of which six were assumed to be constant over the growing season and were fixed based on previous information. The three variable parameters were the initial slope (alpha) and saturation value (gamma) of the light-response curve of carboxylation efficiency in the intercellular cavity, and the cost of transpiration (lambda), in carbon units, regulating the degree of stomatal opening. These parameters could not be estimated independently, nor could their values be satisfactorily found by standard nonlinear regression techniques. A Monte Carlo based simulation procedure was devised to analyze the best-fit parameters and their mutual correlations near the minimum of the residual sum of squares. This was accomplished by replacing the saturation value of the light-response curve with a linearity parameter that determined the shape of the curve. In the best fit solutions, only alpha and lambda varied from day to day, whereas the shape of the curve was constant (i.e., gamma was proportional to alpha). Both alpha and lambda showed consistent patterns from spring to autumn, but the seasonal variation was considerably greater for alpha than for lambda. The optimal stomatal control model with the seven fixed and two daily parameter values gave a good overall fit for photosynthetic rate over the season (PEV > 95%).