Controlled vocabularies for plant anatomical parts optimized for use in data analysis tools and for cross-species studies

Background

It is generally accepted that controlled vocabularies are necessary to systematically integrate data from various sources. During the last decade, several plant ontologies have been developed, some of which are community specific or were developed for a particular purpose. In most cases, the practical application of these ontologies has been limited to systematically storing experimental data. Due to technical constraints, complex data structures and term redundancies, it has been difficult to apply them directly into analysis tools.

Results

Here, we describe a simplified and cross-species compatible set of controlled vocabularies for plant anatomy, focussing mainly on monocotypledonous and dicotyledonous crop and model plants. Their content was designed primarily for their direct use in graphical visualization tools. Specifically, we created annotation vocabularies that can be understood by non-specialists, are minimally redundant, simply structured, have low tree depth, and we tested them practically in the frame of Genevestigator.

Conclusions

The application of the proposed ontologies enabled the aggregation of data from hundreds of experiments to visualize gene expression across tissue types. It also facilitated the comparison of expression across species. The described controlled vocabularies are maintained by a dedicated curation team and are available upon request.

     

Drones for butterfly conservation: larval habitat assessment with an unmanned aerial vehicle

Context

Evidence-based nature conservation focuses on ecological facts and the incorporation of knowledge on the ecology of species, including its entire life cycle. In butterflies, imagos and its larvae often demand specific and diverging micro-habitat structures and resources. In consequence, ecological requirements of the imaginal and pre-imaginal stage have to be taken into consideration to conduct effective conservation management.

Objective

Here we analyse ecological pre-requisites of imagos and larvae for two lycaenid butterfly species, the common blue Polyommatus icarus and the adonis blue Polyommatus bellargus. Both butterfly species occur in calcareous grasslands and mainly depend on two plant species at our study site, the horseshoe vetch Hippocrepis comosa and bird’s-foot trefoil Lotus corniculatus. These plant species serve as nectar sources and larval host plants for the two butterfly species.

Methods

First, we assessed the occurrence of imagines and larvae of the two butterfly species and recorded various micro-habitat characteristics, like the number of flower buds of the two main host plants, the surrounding vegetation height, percentage of bare soil, availability of shadow, and the distance to and geographic direction of thickets at respective sites. In a second step we took high resolution aerial pictures from our study area using an unmanned aerial vehicle (drone). Based on these aerial pictures and the information on the larvae´s habitat preference from our field observations, we trained a habitat suitability model to identify micro-habitat structures suitable for larvae of the two butterfly species.

Results

We found that abundance of imagos is positively correlated with flower bud density of the two host plants. Low vegetation height and high proportion of bare soil (but not flower bud density) positively influence egg oviposition. The calculated habitat suitability models predict the occurrence of high quality larval habitats with high prediction power (AUC = 0.72).

Conclusions

This combined data set consisting of field observations, high resolution aerial pictures taken from an unmanned aerial vehicle, and models underline that (1) species with complex life cycles may request more than one habitat niche, depending its stage of development, and (2) high resolution aerial pictures taken from drones provide valuable background data to generate habitat suitability models—even on a micro scale but covering larger parts of a landscape.

     

Derivation of locally valid estimators of the aboveground biomass of Norway spruce

The carbon (C) stocks of forests are usually calculated from inventory-based estimates of the stem volume, tree-species-specific wood densities, biomass expansion factors (BEF) and functions for the mass of branches and needles/leaves, and the C concentration. However, reported BEFs in the literature are inconsistent, and especially the reliability of the C stock estimates for young stands is unknown. We describe an efficient method for deriving locally valid functions in order to estimate the aboveground biomass of young Norway spruce (Picea abies Karst.) stands. Data were collected from two adjacent stands, representing the treatment Control and Fertilized of an amelioration experiment. The stem volume was derived from Mass Tables as a function of diameter and height and was converted to stem mass with a species-specific conversion factor. Subsamples of branches from different positions within the canopy were selected by probability proportional to size (PPS) sampling. Needles and branches were weighed separately. The obtained expansion functions for branch and needle biomass have dbh as the only input variable and are accurate (0.88<R²<0.96). Earlier published allometric functions carried a considerable bias, especially when applied for young stands. We found that differences in soil fertility do not alter the ratio between the masses of stems, branches, and needles. Regionally derived biomass expansion functions can be used for sites with different soil fertility, can greatly improve the estimate of the aboveground biomass, and can be generated with a modest effort of field and laboratory work.     

Influences of environmental factors on the radial profile of sap flux density in Fagus crenata growing at different elevations in the Naeba Mountains, Japan

Sap flux density was measured continuously during the 1999 and 2000 growing seasons by the heat dissipation method in natural Fagus crenata Blume (Japanese beech) forests growing between 550 and 1600 m on the northern slope of the Kagura Peak of the Naeba Mountains, Japan. Sap flux density decreased radially toward the inner xylem and the decrease was best expressed in relation to the number of annual rings from the cambium, or in relation to the relative depth between the cambium and the trunk center, rather than as a function of absolute depth. The relative influences of radiation, vapor pressure deficit and soil water on sap flux density during the growing season were similar for the outer and inner xylem, and at all sites. Measurements of soil water content and water potential at a depth of 0.25 m demonstrated that sap flux density responded similarly and sensitively to water potential changes in this soil layer, despite large differences in rooting depth at different elevations, localizing one important control point in the functioning of this forest ecosystem. Identification of the relative influences of radiation, vapor pressure deficit and drying of the upper soil layer on sap flux density provides a framework for in-depth analysis of the control of transpiration in Japanese beech forests. In addition, the finding that the same general controls are operating on sap flux density despite climate gradients and large differences in overall forest stand structure will enhance understanding of water use by forests along elevation gradients.     

Long-term development of soil organic carbon and nitrogen stocks after shelterwood- and clear-cutting in a mountain forest in the Bavarian Limestone Alps

Forest soils store large stocks of soil organic matter (SOM) and are of vital importance for the ecosystem supply with nutrients and water. According to the available literature, depending on management regime and site properties, different negative and positive effects of forest management (particularly of forest thinnings and shelterwood cuttings) on soil organic carbon (SOC) and nitrogen (N) stocks are observed. To elucidate the long-term impact of different shelterwood systems and small clear-cuttings on the OC and N stocks of shallow calcareous soils in the Bavarian Alps, we conducted soil humus inventories on different plots of a mixed mountain forest management experiment started in 1976. The silvicultural multi-treatment experiment consists of a NW-exposed Main Experiment (ME) site with eight plots of different cutting intensity (two unthinned controls, two light shelterwood cuttings = 30 % of basal tree area removed, two heavy shelterwood cuttings = 50 % removed, and two clear-cuttings = 100 % removed) on Triassic dolostone. Additionally, plots were installed at a N-exposed dolostone (ND) site and two sites (FL, FH) on Flysch sandstone (each with one unthinned control and one heavy shelterwood cutting). The shelterwood cuttings from 1976 were repeated in 2003 to re-establish the overstorey basal area as produced by the first cutting in the different plots. Thirty-five years after the first treatments, forest floor SOC and N stocks were significantly decreased (up to ?70 %) at the different shelterwood and clear-cut treatments compared to the unthinned control at the ME site despite vigorous development of natural rejuvenation. Also significantly smaller topsoil (forest floor plus mineral soil 0–10 cm depth) OC stocks (between ?16 and ?20 %) were detected at the thinned compared to the control plots. Differences in topsoil N stocks were also considerable (between ?3 and ?14 %), but substantially smaller than OC stock changes. For the total soil down to 30 cm depth, OC stocks in the differently thinned plots were consistently smaller compared to the unthinned control plots. Comparable to our findings at the ME site, heavy shelterwood plots at the three other sites (ND, FL, and FH) showed significant losses of OC in the forest floor (up to 43 %), mineral soil (up to 38 %), topsoil (up to 38 %), and total soil (up to 34 %). Significant large absolute and relative SOC decreases coincided with sites characterized by large initial humus stocks. Moreover, significant effects of heavy shelterwood cuttings on SOC and N stocks (on average 23 % SOC loss and 13 % soil N loss for the forest floor plus the uppermost 10 cm mineral soil) were detected on a regional level. Our results show that different shelterwood systems are accompanied with a considerable long-term decrease in OC and N stocks in shallow calcareous forest soils of the Bavarian Alps. However, a comparison with a windthrown forest stand at a nearby similar site indicates that SOM losses after thinning operations are small compared to decreases following windthrow or other calamities with subsequent large soil erosion and increased mineralization processes.     

Adenylates as an estimate of microbial biomass C in different soil groups

Adenylate (i.e. adenosine tri- (ATP), di- (ADP) and monophosphates (AMP)) and microbial biomass C data were collected over a wide range of sites including forest floor layers and forest, grassland and arable soils. Microbial biomass C was measured by fumigation extraction and adenylates after alkaline Na₃PO₄/DMSO/EDTA extraction and HPLC detection. Our aims were (1) to test whether the sum of adenylates is a better estimate for microbial biomass than the determination of ATP, (2) to compare our conversion values with those proposed by others, and (3) to analyse whether soil properties or land use form affect the relationships between ATP, adenylates and microbial biomass C. A close relationship was found between microbial biomass C and ATP (r=0.96), but also with the sum of adenylates (r=0.96) within all appropriately conditioned soil samples (n=112). In the mineral soil (n=98), the geometric means of the ATP-to-microbial biomass C ratio and the adenylates-to-microbial biomass C ratio were 7.4 and 11.4 μmol g⁻¹, respectively. The mean ratios did not differ significantly between the different texture classes and land use forms. In the forest floor, the ATP-to-microbial biomass C ratio and the adenylates-to-microbial biomass C ratio were both roughly two-thirds of those of the mineral soil. The average adenylate energy charge (AEC) of all soil samples was 0.79 and showed a strong negative relationship with the soil pH (r=−0.69). However, the AEC is presumably only indirectly affected by the soil pH.     

Einfluß des Bodengefüges auf Wurzelwachstum und Phosphataufnahme von Sommerweizen

Influence of Soil Structure on Root Growth and P Uptake of Spring Wheat The effect of soil structure (fine aggregat, coarse aggregate and compacted structure) on root growth, root morphology, and P availability of spring wheat (Triticum aestivum L.) was studied in pot and split root experiments using three soils (2 × Alfisol-Udalf, Alluvium). CAL-soluble P was 63–90 mg P · kg^?1 soil, indicating a sufficient P supply. Root length, root surface, root fresh weight, shoot weight, and seed yield were decreased due to coarse aggregate and compacted structure. Roots were significantly thickened and roots hairs were longer in the fine aggregate structure than in the compacted and coarse aggregate structures. P concentration in the shoot and P uptake of spring wheat growing in the coarse aggregate and compacted structure were lower because root growth was decreased. In the split root experiment, in contrast to pot experiment, P uptake was lower in the compacted than in the fine aggregate treatment. The results demonstrate that P availability was influenced by soil structure via the influence on root growth and thus access of roots to P.     

Local extinctions of the wetland specialist Swertia perennis L. (Gentianaceae) in Switzerland: a revisitation study based on herbarium records

We studied population extinction of the locally abundant fen plant Swertia perennis in Switzerland and used up to 127-year old herbarium records to relocate 63 sites that had once hosted this species. We recorded current site characteristics and related them to the absence or abundance of populations. Fifty-four sites (86%) were still traditionally used (extensively mown or grazed). Fifteen populations (24%) had gone extinct. Extinction was more likely at lower altitude, in the peripheral distribution range of S. perennis (58% peripheral, 9% central populations extinct), on the smallest fens (75% extinct on fens <400 m²) and on fens with intensified land use. However, even on traditionally managed wetlands 18.5% of the populations had gone extinct. Moreover, 40% of all remaining populations were smaller than 250 flowering plants. We conclude that both intensified agricultural practice and habitat fragmentation contributed to local extinction of S. perennis. Small populations, especially, may not be able to persist in the long term.     

Phytoextraction of heavy metal contaminated soils with Thlaspi goesingense and Amaranthus hybridus: Rhizosphere manipulation using EDTA and ammonium sulfate

Selection of appropriate plant species and rhizosphere manipulation to enhance metal uptake are considered key factors in the development of phytoextraction technologies. A pot trial was conducted with two contaminated soils to investigate the effect of EDTA and ammonium sulfate on the accumulation of heavy metals into shoots of the low‐biomass hyperaccumlator Thlaspi goesingense Hálácsy (Brassicaceae) and the high‐biomass non‐hyperaccumulating plant Amaranthus hybridus (Amaranthaceae). Upon application of 1 g EDTA (kg soil)^—1 metal extractability with 1 M NH₄NO₃ increased substantially, whereas the application of (NH₄)₂SO₄ was less effective. The EDTA treatment increased the heavy metal concentrations in both plant species, however, the difference to the control was larger for A. hybridus. EDTA enhanced shoot concentrations in A. hybridus grown on soil Arnoldstein from 32.7 mg kg^—1 to 1140 mg kg^—1 for Pb and from 3.80 mg kg^—1 to 10.3 mg kg^—1 for Cd. Cd concentrations in shoots of T. goesingense were also increased by EDTA application, however, a slight decrease was observed for Pb. T. goesingense accumulated 2840 mg Pb kg^—1 without any treatment. This is the first report of Pb hyperacumulation by T. goesingense. A decrease of shoot Pb concentration was observed in T. goesingense upon treatment with ammonium sulfate. Although metal concentrations in the shoots were rather large and significantly increased upon application of EDTA, plant growth and heavy metal removal were still too small to obtain reasonable extraction rates in soils heavily polluted by metals. It should be also noted that metal lability largely increased in EDTA‐treated soils and this lability persisted for several weeks after the application of the chelating agent, which is likely to be associated with the risk of groundwater contamination.