Comparative analysis of three chemometric techniques for the spectroradiometric assessment of canopy chlorophyll content in winter wheat

Hyperspectral data sets contain useful information for characterizing vegetation canopies not previously available from multi-spectral data sources. However, to make full use of the information content one has to find ways for coping with the strong multi-collinearity in the data. The redundancy directly results from the fact that only a few variables effectively control the vegetation signature. This low dimensionality strongly contrasts with the often more than 100 spectral channels provided by modern spectroradiometers and through imaging spectroscopy. With this study we evaluated three different chemometric techniques specifically designed to deal with redundant (and small) data sets. In addition, a widely used 2-band vegetation index was chosen (NDVI) as a baseline approach. A multi-site and multi-date field campaign was conducted to acquire the necessary reference observations. On small subplots the total canopy chlorophyll content was measured and the corresponding canopy signature (450-2500 nm) was recorded (n_obs = 42). Using this data set we investigated the predictive power and noise sensitivity of stepwise multiple linear regression (SMLR) and two ‘full spectrum’ methods: principal component regression (PCR) and partial least squares regression (PLSR). The NDVI was fitted to the canopy chlorophyll content using an exponential relation. For all techniques, a jackknife approach was used to obtain cross-validated statistics. The PLSR clearly outperformed all other techniques. PLSR gave a cross-validated RMSE of 51 mg m⁻² for canopy chlorophyll contents ranging between 38 and 475 mg m⁻² (0.99 ≤ LAI ≤ 8.74 m² m⁻²). The lowest accuracy was achieved using PCR (RMSE_cv = 82 mg m⁻² and ). The NDVI, even using chlorophyll optimized band settings, could not reach the accuracy of PLSR. Regarding the sensitivity to artificially created (white) noise, PCR showed some advantages, whereas SMLR was the most sensitive chemometric technique. For relatively small, highly multi-collinear data sets the use of partial least square regression is recommended. PLSR makes full use of the rich spectral information while being relatively insensitive to sensor noise. PLSR provides a regression model where the entire spectral information is taken - in a weighted form - into account. This method seems therefore much better adapted to deal with potentially confounding factors compared to any 2-band vegetation index which can only avoid the most harmful factor of variation.     

Presence of opportunistic bacteria (Rhizobium spp.) with potential for molecular misdiagnosis among canine and feline clinical samples

Rhizobium radiobacter was detected in 12 of 187 dogs and 2 of 100 cats using a polymerase chain reaction (PCR) assay formerly designed for the Rickettsia genus. Although PCR primers used for pathogenic infectious agents are specifically assessed to avoid cross-amplification, this retrospective study highlights the importance of sequencing to avoid molecular misdiagnosis.     

Nutritive value of some tropical grasses used by traditional small farms in the highlands of Burundi

The objective was to estimate—according to the French feeding system—the nutritive value of three tropical grasses (Eragrostis olivacea, Setaria sphacelata and Tripsacum laxum) used in traditional small farms of Burundi. Dry matter (DM) yield was monitored on anti-erosive hedges or on small fields in 60 small farms for eight consecutive years. DM intake and digestibility values were measured on seven steers or seven male sheep. Degradability values were determined on three sheep. S. sphacelata exhibited higher DM yield (t ha⁻¹), energy (UF, kg⁻¹ DM) and protein (PDI, g kg⁻¹ DM) values (17.3, 0.73 and 68, respectively) than T. laxum (9.11, 0.64 and 47) and E. olivacea (not determined, 0.46 and 42). The UF and PDI intakes of these grass species were able to meet only 51% to 92% of the energy and 59% to 133% of the protein requirements for maintenance of the experimental animals.     

Integrating landscape ecology and conservation physiology

The need to understand how anthropogenic landscape alteration affects fauna populations has never been more pressing. The importance of developing an understanding of the processes behind local extinction is widely acknowledged, but inference from spatial patterns of fauna distribution continues to dominate. However, this approach is limited in its ability to generate strong predictions about future distributions and local extinctions, especially when population-level responses to landscape alteration are subject to long time lags. We review the potential for indices of physiological stress and condition to contribute to understanding of how landscape pattern affects species persistence. Such measures can indicate habitat quality from the perspective of the individual animal, and can reveal environmental stressors before their negative consequences begin to manifest at a population level. Spatial patterns of chronic stress may therefore yield valuable insight into how landscape alteration influences species. We propose that the emerging disciplines of conservation physiology and macrophysiology have much to offer spatial ecology, and have great potential to reveal the physiological pathways through which habitat alteration affects fauna populations and their persistence in fragmented landscapes.     

Multiple disturbance patterns and population structure of a tropical tree species,Afzelia africana (Leguminosae–Caesalpinioideae), in two contrasting bioclimatic zones of the Republic of Benin

Understanding how multiple disturbances affect species population structure is crucial for designing a better conservation strategy of threatened species. In this paper, we assessed the disturbance patterns and evaluated their effects on the population structure of Afzelia africana, in two different bioclimatic zones of the Republic of Benin. The main disturbances in the studied area included branch pruning and debarking. Individuals of medium size (20–40 cm) were mostly pruned and debarked. The percentages of pruning and debarking were similar at population level across the two studied bioclimatic zones (t = ?0.04, p = 0.96; t = 0.73, p = 0.48). Examining this at individual level, pruning was similar but debarking was higher in the Sudanian zone (12.14 ± 0.93%) than in the Sudano-Guinean zone (7.44 ± 0.88) (W = 40859, p < 0.001). Population structure was bell-shaped in the Sudanian zone regardless of the disturbance level. In contrast, in the Sudano-Guinean zone, mildly disturbed populations showed an inverse J-shaped structure, whereas those highly disturbed were bell-shaped. This underlined the climatic (dryness) and disturbance effects on the establishment and recruitment of small trees into the next life stage in tropical savanna ecosystems. Good regeneration pattern and the largest individuals were found within the protected areas, demonstrating the prominent role of protected areas for the species conservation. Therefore, we suggested that conservation efforts should be extended to populations outside the protected areas. Forestry department should establish firebreaks networks to protect small individuals and facilitate their recruitment, as well as the regulation and enforcement should be improved on the sustainable use of the species.     

Intra- and inter-provenance variability in phloem phenols of Picea abies and relationship to a bark beetle-associated fungus

One hundred Norway spruce (Picea abies (L.) Karst.) clones (three ramets per clone) were analyzed for phloem phenol composition and concentration before and 10 days after wound inoculation with sterile malt agar. Fifty clones (Experiment 1) belonged to the same provenance, whereas the remaining clones (Experiment 2) belonged to five provenances from three geographic areas. In Experiment 2, two additional ramets from the same clones were mass inoculated with Ceratocystis polonica (Siem.) C. Moreau to quantify the resistance of each clone. Tree response to wound inoculations was characterized by increased catechin concentration in both experiments, accompanied by increases in astringin and decreases in piceid in Experiment 1. In both experiments, we observed a diverse group of phenolic compounds whose concentrations increased (catechin, astringin) or did not vary (taxifolin glucoside) in response to wound inoculations, whereas concentrations of a homogeneous group of stilbene compounds decreased (piceid) or did not vary (isorhapontin, unidentified stilbene). In Experiment 2, provenances from the alpine and Hercynian-Carpatic areas differed from provenances from the Baltic area with respect to the relative importance of these two groups of compounds, further indicating that the two groupings of phenolic compounds structure the Norway spruce populations. Eighty days after mass inoculation, the percentage of healthy sapwood, which was taken as a measure of tree resistance, indicated that clones from the Baltic area were less resistant to mass inoculations than clones from the alpine and Hercynian-Carpatic areas. We conclude that the degree of resistance of Norway spruce trees to mass inoculations with a bark beetle-associated fungus can be predicted based on the diversity of constitutive phloem phenols and the ability to induce phenol synthesis in response to wounding.     

Activation of stress-responsive mitogen-activated protein kinase pathways in hybrid poplar (Populus trichocarpa x Populus deltoides)

Plant mitogen-activated protein kinase (MAPK) cascades are important amplifying modules that can rapidly transduce stress signals into various appropriate intracellular responses. Several extracellular regulated kinase (ERK)-type MAPKs involved in plant defense signaling have been identified in herbaceous species, but no MAPK cascade has yet been characterized in a tree species. We examined the signal transduction events that lead to activation of defense mechanisms in poplar, a major forest species of economic and ecological importance which is becoming the model tree system for studying stress and adaptation responses. We show that, in poplar cell suspensions and leaf tissue, chitosan, a non-host-specific elicitor, and ozone, a strong oxidant and atmospheric pollutant, induce rapid and transient activation of at least two myelin basic protein (MBP) kinases with apparent molecular masses of 44 and 47 kD. The chitosan- and ozone-activated kinases have characteristics of MAPKs-they preferentially phosphorylate MBP, require tyrosine and threonine phosphorylation to be activated and are specifically recognized by anti-ERK and anti-pERK antibodies. Moreover, activation of these poplar MAPKs by chitosan or ozone is dependent on the production of reactive oxygen species; the influx of calcium ions via membrane channels; the activation of an upstream, membrane-localized component; and a cognate MAPK kinase (MAPKK). These data suggest that biotic and abiotic challenges activate MAPKs in poplar, as in herbaceous species, which then function as a convergence point for pathogen defense and oxidant stress signaling cascades.