Spatial analysis of genetic diversity as a tool for plant conservation

Development of suitable approaches to the analysis of genetic diversity in a spatial context, where factors such as pollination, seed dispersal, breeding system, habitat heterogeneity and human influence are appropriately integrated, can provide new insights in the understanding of the mechanisms of maintenance and dynamics of populations. In this sense, it is important to recognise that patterns and processes may take place at different scales at the same time, and that the scales of a study must be chosen in accordance with the objectives pursued. Apart from conventional approaches to genetic structure, spatial autocorrelation and related techniques, such as Mantel test, correlograms, Mantel correlograms, join-counts, variograms and point pattern analysis, can detect and characterise the existence of spatial genetic structures and lead the way to discussing the environmental and biological factors responsible for them. An alternative way of including spatial variability in modelling approaches that deal with genetic patterns or processes is through the use of constrained ordinations. Although scarcely used at present, these methodologies have great applicability in conservation biology and can lead a way to an effective integration of genetic, demographic and ecological perspectives.     

Vital rate sensitivity analysis as a tool for assessing management actions for the desert tortoise

Sensitivity analyses of population growth in desert tortoise (Gopherus agassizii) have shown no consensus on the limiting vital rate. More importantly, the most sensitive vital rate might not be the most readily manipulated by management, so it begs the question of what actions would be most effective. We compared 13 management alternatives using a vital rate sensitivity analysis that is valid regardless of age structure, and is sensitive to initial population size and time frame, to determine the efforts required for equivalent population growth. We evaluated three time frames, each with five initial population sizes and three initial age distributions. To achieve equivalent population growth, mortality of older females needed to be reduced less than did mortality of other age classes. Similarly, fewer adults needed to be introduced to a population to have the same effect as releasing juveniles, but differences among adult age classes were trivial. A single release (headstarting) required fewer total individuals than did annual releases to achieve the same population growth. Also, the same population growth was more easily achieved when the initial age structure was deficient of young animals. Interestingly, because small tortoises are difficult to survey, some management alternatives could result in increased population size but decreased numbers of countable individuals over short to intermediate (25 years) time frames. Our paper demonstrates an approach to determine what constitutes equivalent management actions for population growth, thus allowing managers to more directly compare expected gains toward population recovery achieved by their resource-allocation decisions.     

Soil reflectance as a generic tool for assessing infiltration rate induced by structural crust for heterogeneous soils

Raindrop energy disintegrates soil aggregates and rearranges soil particles to form a structural crust on the upper soil layer. The structural crust affects the physical properties of the soil, which can be observed by significant colour changes on the soil surface. Spectral differences observed in the structural crust are caused by rearrangement of the soil surface texture, mainly an increase in the clay fraction. Previous studies conducted on crusted soils using reflectance spectroscopy were limited to a certain soil type or area and seemed to be strongly dependent on the small range of soil types. In the current study, the influence of raindrop energy on the NIR‐SWIR spectral reflectance (1200–2400 nm) of heterogeneous soils was evaluated and used in combination with partial least squares (PLS) regression to construct a model that correlates the infiltration rate (IR) with its reflectance. Four soils from Israel and three soils from the USA were studied to provide a single data set. A relatively small root mean square error of cross‐validation (RMSECV) of 15.2% was found. A ratio of prediction to deviation (RPD) value of 1.98 indicates a promising generic model. Additionally, PLS models were run on different combinations of soil types (RPD values ranging between 2.4 and 3.2). For all models, whether all soils were run in one cross‐validation data set, or run for different combinations of soils, the best assessment of IR was achieved when using reduced wavelength range (selected wavelengths based on Martens’ significance test selection). These results allowed us to conclude that a generic approach aimed at assessing the structural crust for a variety of soils is feasible. A generic model using the suggested spectral approach has the potential to provide NIR‐SWIR spectral soil IR predictions with either a local or global data base of soils worldwide and may contribute to improved protection of crusted soils from erosion or water loss by runoff.     

Ion-exchange chromatography as a tool for investigating vanadium speciation in sediments: preliminary studies

Journal of Soils and Sediments - We conducted this investigation in order to develop a simple method for the determination of bioavailable vanadium and its speciation within sediments. The...     

C and N NMR spectroscopy as a tool in soil organic matter studies

Nuclear magnetic resonance (NMR) is a valuable tool for the characterization of soil organic matter and humification processes in soils. This review highlights soil organic matter studies based mainly on solid-state ¹³C and ¹⁵N NMR spectroscopy and some emerging applications, that may provide significant progress in our knowledge on soil organic matter. A major advantage of Nmr spectroscopy is that it can be used as a non-invasive method for solid soil samples or soil fractions. Although resolution is limited, one can obtain an overview on the organic matter structures present in the soil sample. Application of ¹³C and ¹⁵N NMR to soils has, for a long time, been confined to the study of bulk soils or humic extracts for structural characterization. The transformations of soil organic C and N are now being investigated after addition of ¹³C- and ¹⁵N-labelled parent materials to the soil and following their evolution in different C and N pools. With labelling techniques it is also possible to study the interaction of organic pollutants with soil organic matter. Contamination of a soil with man-made additives, such as soot or brown coal dust, can also be detected in soils or individual soil fractions.     

Large‐scale soil maps and a supplementary database for land use planning in Estonia

A soil map at the scale 1:10,000 serves as a major important document for land owners and local governments, which allows them to use soil information in their daily activity. The intensity of exploitation of soil maps will increase when the very map and its legend are supplemented, within colored and indexed polygons, with information about soil texture and reaction by layers, but also about the thickness and characterization of the epipedon, quality indices for soil assessment, classes of stoniness, and prevalent fractions of stones, erosion risk, etc. Special maps of agronomical status, with a list of proper measures for improvement of soils and their associations, should form a regular component of large‐scale mapping. As decrease in arable land and increase in the forest area are common trends in land use, these maps and general soil data should serve as the fundamental source of information for decision making concerning land use. Data indicating the suitability of any soil for any crop should be entered in a database. Application of GIS on any level of national economy, digitization of a large‐scale soil database and making it accessible to land users would allow to expand the amount of available information for each soil map polygon.     

Predicting alpha, beta and gamma plant diversity from physiognomic and physical indicators as a tool for ecosystem monitoring

We searched for predictive models for alpha, beta and gamma plant diversity based in easy to measure field indicators. The study was conducted on the upper belt of the Córdoba mountains (Argentina). We established 222 permanent plots of 4 × 4 m distributed on sites with different physiognomy, topography and management. At each plot we measured physical and physiognomic indicators and recorded the presence of all vascular plants. We estimated alpha diversity as the number of species detected in a plot, beta diversity as the floristic dissimilarity between two plots, and gamma diversity as the number of species detected in a landscape. Through linear regression we found predictive models for alpha and pair-wise beta diversity. Then we analysed if predicted average alpha and beta diversity were good estimators of gamma diversity. We recorded a total of 288 species (5-74 species per plot). Alpha diversity was highest in sites on shallow soils with high structural richness (i.e. high number of cover categories), half covered by lawns, at sunny slopes and rough landscapes (r² = 0.66). For beta diversity, the difference between plots in structural richness and in cover of thick tussocks grasses and lawns were the best predictors (r² = 0.45). For different sets of simulated landscapes, gamma diversity was well explained by predicted average alpha and beta diversity, plus the sampling effort (r² = 0.92). We concluded that using easy to measure field indicators it is possible to estimate plant diversity at different levels with a good accuracy.     

Mineralisation and humification of plant matter in soil samples as a tool in the testing of soil quality

Since life is inevitably dependent on the assimilation and dissimilation of carbon, and since most of the organic carbon is bound in soil humic matter, the mineralisation and humification of plant carbon in soil should be monitored, so as to evaluate soil quality and avoid ecological risks. For this reason we suggested an incubation test of thirty days in duration with soil samples amended or not with lucerne meal as a source of plant carbon. During the incubation period, CO₂ release is to be measured repeatedly, and thereafter contents of humic acids (HA) and fulvic acids (FA) should be estimated and compared with those determined in the original soil samples. Our results obtained with samples from non-fertilized or long-term (?>?40 years) fertilized plots of two field trials indicate that fertilization by NPK?+ farm yard manure resulted in (i) a slight enhancement of C mineralisation, i.e., CO₂ release from soil, and (ii) a significant increases of HA and FA contents. Soil samples from a reclaimed mine spoil, and either fertilised or not with sewage sludge did not show distinct differences in the same parameters. The practicability of the incubation test as a tool in the monitoring of soil quality should be further proved using samples from differently affected soils.     

Coastal land scalding in NSW,Australia: soil chemical characteristics and their implications for remediation of the scalded lands

Scalded lands are common in acid sulphate soil areas on the New South Wales coast, Australia. In this work, chemical characteristics of the scalded acid sulphate soils at nine sites along this coast were investigated. The investigated acid sulphate scalds are characterized by an extremely acidified topsoil layer (0–0.6 m) although they derive from the sediments of varying salinity and the metal sulphides contained in the soils have experienced different degrees of oxidation. Almost all of the investigated scalds occur in the areas that have a lower surface elevation than the surrounding areas. These hollows may act as sinks for acid sulphate materials and salts that are transported from the surrounding areas and the shallower watertables in such locations may enhance upward transport of acid and salt materials from the underlying oxidized sulphidic sediments. In general, the scalded acid sulphate soils have less organic matter and soluble phosphorus, and a greater salinity, soluble acidity, soluble Al, Mn and Zn concentrations, compared to the adjacent non‐scalded acid sulphate soils. These are most likely soil constraints for revegetation of the scalded lands and treatment will need to involve acid neutralization (e.g. application of lime) and addition of P fertilizers to reduce the soluble acidity, immobilize soluble Al, Mn and Zn, and increase P availability. The evidence also shows that the higher soluble Al concentration in the scalded soils, relative to the non‐scalded soils, is related to their lower organic matter content. Hence, rehabilitation of these scalded lands should involve the addition of organic matter to reduce soluble Al concentrations; it may also help reduce Mn and Zn toxicity, and salinity. Copyright © 2001 John Wiley & Sons, Ltd.     

Ecogeographical distribution of wild, weedy and cultivated Sorghum bicolor (L.) Moench in Kenya: implications for conservation and crop-to-wild gene flow

The potential gene flow between a crop and its wild relatives is largely determined by the overlaps in their ecological and geographical distributions. Ecogeographical databases are therefore indispensable tools for the sustainable management of genetic resources. In order to expand our knowledge of Sorghum bicolor distribution in Kenya, we conducted in situ collections of wild, weedy and cultivated sorghum. Qualitative and quantitative morphological traits were measured for each sampled wild sorghum plant. Farmers’ knowledge relating to the management of sorghum varieties and autecology of wild sorghum was also obtained. Cluster analysis supports the existence of several wild sorghum morphotypes that might correspond to at least three of the five ecotypes recognized in Africa. Intermediate forms between wild and cultivated sorghum belonging to the S. bicolor ssp. drummondii are frequently found in predominantly sorghum growing areas. Crop-wild gene flow in sorghum is likely to occur in many agroecosystems of Kenya.     

Electron paramagnetic resonance (EPR) spectroscopy as a tool for the characterization of biochar from guava waste

Journal of Soils and Sediments - The ability of biochars prepared from pyrolysis of guava pulp and seed industrial wastes to form complexes with the ions vanadyl (VO2+), a Pearson hard acid, and...     

An information retrieval system for VIR's herbarium, St. Petersburg, Russia, as a tool for cultivated plant research

The herbarium collection of the N.I. Vavilov Institute of Plant Industry (WIR) contains specimens of cultivated plants, their wild relatives and weedy plants and provides ample opportunities for research. It is a unique special herbarium collection and one of those rare collections having a card index (catalog). For the catalog to be functional, it should reflect the current changes in the taxa names. Only a computerized card file may meet this requirement. The creation of a database for VIR's herbarium was launched in 1995. VIR is carrying out a range of work necessary for providing a wider access to its herbarium and related information for the international scientific community.     

ED-XRF as a tool for rapid minerals control in milk-based products

An ED-XRF method for the rapid determination of a series of analytes (phosphorus, sulfur, chlorine, potassium, calcium, iron, zinc) in milk-based products has been developed and validated. The investigated samples were commercial products obtained from various parts of the world. Reference values measured by inductively-coupled plasma-optical emission spectroscopy and by potentiometry for chloride were used to calibrate the ED-XRF. Calibrations were established with 30 samples, and validation was made using a second set of 30 samples. An evaluation of this alternative method was done by comparison with data from the reference methods. Pellets of 4 g were prepared under 2 tons of pressure. For each sample, 3 pellets were prepared and analyzed. Limits of quantification and repeatabilities were evaluated for the described analytes.     

Dynamic interfacial rheology as a tool for the characterization of whey protein isolates gelation at the oil-water interface.

Heat-induced interfacial aggregation of a whey protein isolate (WPI), previously adsorbed at the oil-water interface, was studied by interfacial dynamic characteristics coupled with microscopic observation and image analysis of the drop after heat treatment. The experiments were carried out at temperatures ranging from 20 to 80 degrees C with different thermal regimes. During the heating period, competition exists between the effect of temperature on the film fluidity and the increase in mechanical properties associated with the interfacial gelation process. During the isothermal treatment, the surface dilational modulus, E, increases, and the phase angle, delta, decreases with time to a plateau value. The frequency dependence of E and delta is characteristic of viscoelastic films with increasing delta and decreasing E at lower frequencies. The effects of heat treatment depend on the conditions at which the gelation process takes place. Microscopic observation of gelled films gives complementary information on the effect of heat treatment on WPI adsorbed films.     

Soil‐vegetation relationships of three arid land plant species and their use in rehabilitating degraded sites

It is essential to consider soil characteristics when establishing vegetation in arid lands. In this study, the redundancy analysis (RDA) ordination method was used in this study to evaluate the habitats of Halocnemum strobilaceum, Limonium iranicum and Tamarix passerinoides growing in the Sejzy region, east of Isfahan. The study area was stratified into six ecologic‐floristic complexes. Stratified random sampling was then employed to collect soil and vegetation data from 1‐ha quadrats on nine sites. The soil samples were analysed to determine the characteristics of the soil in which the three species grew and to examine the soil profiles up to a depth of 2 m. Soil analyses revealed that high amounts of gypsum, silt, clay, saline, alkali and sulphate in the soil constituted a favourable habitat for Halocnemum strobilaceum. However, the per cent of silt and sulphate concentration in deep layers were negatively correlated with the growth of this species. Evaluation of the L. iranicum habitat revealed that the amounts of carbonate and CCE in the topsoil were positively correlated with the establishment and growth of the species but salinity and alkalinity were negatively correlated. The primary soil characteristics that positively influenced T. passerinoides included the presence of organic matter and bicarbonate ions in the soil layers and the total Ca and Mg content of the topsoil. However, Na was negatively correlated with Tamarix species. Determination of the soil characteristics that are associated with each of these xerophytic species can be used to determine which species is suitable for rehabilitating degraded sites in the study area. Copyright © 2010 John Wiley & Sons, Ltd.     

Human gene expression as a tool to determine horticultural maturity in a bioactive plant (Echinacea purpurea L. Moench)

A phenological study was conducted to determine the impact of harvest maturity on the immune-modulating properties of Echinacea purpurea. The aerial parts of this plant were collected during seven stages of development and were assayed for a common botanical marker for this species, cichoric acid. Plants of selected development stages were also assayed for total polysaccharides and compared for their immune-modulating effects on the THP-1 monocyte/macrophage cell line by means of a gene expression study. Although the concentration of cichoric acid did not change significantly during the course of the study, stage 1 (advanced vegetative) had the highest concentration of total polysaccharides and exhibited the most potent induction activity on immune-modulating cytokines such as interferon-gamma and tumor necrosis factor-alpha. These findings suggest that the use of gene expression may be an effective tool not only to standardize botanical extracts but also to optimize harvest time.     

The suitability of weed risk assessment as a conservation tool to identify invasive plant threats in East African rainforests

We tested the ability of an international Weed Risk Assessment (WRA) protocol to predict invasion status of 230 alien plant species introduced via a botanical garden to tropical rainforest in Tanzania. The reliability and accuracy of WRA in discriminating between invaders and non-invaders was independently assessed using field data on species demography and distribution. The WRA rejected 83% of known invaders, and accepted 74% of non-invaders. Only 1% of accepted species were known invaders at the site. WRA performance varied among different growth forms, and underestimated the risks arising from palm species. Among those species that had naturalised, the WRA was better at identifying invaders of open rather than forest habitats. The WRA score was significantly correlated with how widespread species had become at the site, suggesting some capacity to predict spatial spread at a landscape scale. Knowledge of propagule pressure and residence time did not increase explanatory power. These results indicate that the WRA was able to discriminate between invaders and non-invaders with accuracy comparable to similar assessments in temperate and sub-tropical regions. It could be made more effective by weighting traits important in tropical forests e.g. certain growth forms, shade tolerance etc. more heavily. Such a modified WRA could be used successfully elsewhere in the palaeotropics as a screening tool to identify the risk of invasion arising from plants introduced for agroforestry, horticulture or landscaping. Given the increasing pressures on tropical forests and importance of agroforestry to local economies, the WRA protocol represents a useful conservation tool.