Visible and near infrared spectroscopy in soil science

This chapter provides a review on the state of soil visible–near infrared (vis–NIR) spectroscopy. Our intention is for the review to serve as a source of up-to date information on the past and current role of vis–NIR spectroscopy in soil science. It should also provide critical discussion on issues surrounding the use of vis–NIR for soil analysis and on future directions. To this end, we describe the fundamentals of visible and infrared diffuse reflectance spectroscopy and spectroscopic multivariate calibrations. A review of the past and current role of vis–NIR spectroscopy in soil analysis is provided, focusing on important soil attributes such as soil organic matter (SOM), minerals, texture, nutrients, water, pH, and heavy metals. We then discuss the performance and generalization capacity of vis–NIR calibrations, with particular attention on sample pre-tratments, co-variations in data sets, and mathematical data preprocessing. Field analyses and strategies for the practical use of vis–NIR are considered. We conclude that the technique is useful to measure soil water and mineral composition and to derive robust calibrations for SOM and clay content. Many studies show that we also can predict properties such as pH and nutrients, although their robustness may be questioned. For future work we recommend that research should focus on: (i) moving forward with more theoretical calibrations, (ii) better understanding of the complexity of soil and the physical basis for soil reflection, and (iii) applications and the use of spectra for soil mapping and monitoring, and for making inferences about soils quality, fertility and function. To do this, research in soil spectroscopy needs to be more collaborative and strategic. The development of the Global Soil Spectral Library might be a step in the right direction

Effects of soil sample pretreatments and standardised rewetting as interacted with sand classes on Vis-NIR predictions of clay and soil organic carbon

Numerous studies have examined the soil analytical potential of diffuse reflectance spectroscopy in the near infrared range, alone or combined with the visible range (Vis-NIR). Soil organic matter (SOM), soil organic carbon (SOC) and clay content are the most commonly and successfully predicted parameters, but predictions are quite variable due e.g. to the range of soil types covered by the calibrations. Especially organic matter predictions are also suggested to be influenced by for example soil moisture content and inclusion of the visible range in the calibration. Excess quartz sand is also suggested to have a negative influence. This study was undertaken to examine the effect of a selection of standardised sample pretreatment procedures, including rewetting, on predictions of clay and SOC content. A subset of 400 samples was selected from a dataset of 3000 Swedish agricultural soils to cover clay and organic matter contents without co-variation. The selected samples were analysed by NIR and Vis-NIR on air-dry samples, either carefully mixed to avoid stratification of particle size classes or shaken to promote separation, resulting in predominantly larger particles being analysed. Unshaken samples were also analysed immediately after standardised additional drying at 35°C for 12 hours and stepwise volumetric rewetting up to 30%. Shaking and additional drying had small negative effects on clay predictions, while drying only had small positive effects on SOC predictions. Volumetric rewetting to 20 or 30% before scanning reduced clay prediction errors by up to 15%, RMSEP reduced from 5.4 % clay to 4.5 % clay, and SOC prediction errors by up to 30%, from 0.9 % SOC to 0.6 % SOC, indicating that standardised rewetting should be considered. The mechanisms concerned could not be specifically identified, but known bands for water, hydroxyl and clay mineral-dependent absorption near 1400, 1900 and 2200 nm were involved in the improved clay calibrations and bands near 1700, 2000, 2300 and 2350 nm in the improved SOC calibrations. The SOC predictions were most inaccurate for soils with a high sand content. For these samples the average prediction error was more than twice as high as those for less sandy samples. Rewetting eliminated this bias, largely explaining the positive effects of rewetting

On-line Vis-Nir sensor determination of soil variations of sodium, potassium and magnesium

Among proximal measurement methods, visible and near infrared (Vis-Nir) spectroscopy probably has the greatest potential for determining the physico-chemical properties of different natural resources, including soils. This study was conducted to determine the sodium, potassium and magnesium variations in a 10. Ha field located in Karacabey district (Bursa Province, Turkey) using an on-line Vis-Nir sensor. A total of 92 soil samples were collected from the field. The performance and accuracy of the Na, K and Mg calibration models was evaluated in cross-validation and independent validation. Three categories of maps were developed: 1) reference laboratory analyses maps based on 92 points 2) Full-data point maps based on all 6486 on-line points Vis-Nir predicted in 2013 and 3) full- data point maps based on all 2496 on-line points Vis-Nir predicted in 2015. Results showed that the prediction performance in the validation set was successful, with average R2 values of 0.82 for Na, 0.70 for K, and 0.79 for Mg, average root mean square error of prediction (RMSEP) values of 0.02% (Na), 0.20% (K), and 1.32% (Mg) and average residual prediction deviation (RPD) values of 2.13 (Na), 0.97 (K), and 2.20 (Mg). On-line field measurement was also proven to be successful with validation results showing average R2 values of 0.78 (Na), 0.64 (K), and 0.60 (Mg), average RMSEP values of 0.04% (Na), 0.13% (K), and 2.19% (Mg) and average RPD values of 1.57 (Na) 1.68 (K) and 1.56 (Mg). Based on 3297 points, maps of Na, K and Mg were produced after N, P, K and organic fertilizer applications, and these maps were then compared to the corresponding maps from the previous year. The comparison showed a variation in soil properties that was attributed to the variable rate of fertilization implemented in the preceding year

Agricultural scene understanding, volume 1

There are no author-identified significant results in this report

Use of high-dimensional spectral data to evaluate organic matter, reflectance relationships in soils

Recent breakthroughs in remote sensing technology have led to the development of a spaceborne high spectral resolution imaging sensor, HIRIS, to be launched in the mid-1990s for observation of earth surface features. The effects of organic carbon content on soil reflectance over the spectral range of HIRIS, and to examine the contributions of humic and fulvic acid fractions to soil reflectance was evaluated. Organic matter from four Indiana agricultural soils was extracted, fractionated, and purified, and six individual components of each soil were isolated and prepared for spectral analysis. The four soils, ranging in organic carbon content from 0.99 percent, represented various combinations of genetic parameters such as parent material, age, drainage, and native vegetation. An experimental procedure was developed to measure reflectance of very small soil and organic component samples in the laboratory, simulating the spectral coverage and resolution of the HIRIS sensor. Reflectance in 210 narrow (10 nm) bands was measured using the CARY 17D spectrophotometer over the 400 to 2500 nm wavelength range. Reflectance data were analyzed statistically to determine the regions of the reflective spectrum which provided useful information about soil organic matter content and composition. Wavebands providing significant information about soil organic carbon content were located in all three major regions of the reflective spectrum: visible, near infrared, and middle infrared. The purified humic acid fractions of the four soils were separable in six bands in the 1600 to 2400 nm range, suggesting that longwave middle infrared reflectance may be useful as a non-destructive laboratory technique for humic acid characterization

Isotopes in pyrogenic carbon: a review

Pyrogenic carbon (PC; also known as biochar, charcoal, black carbon and soot) derived from natural and anthropogenic burning plays a major, but poorly quantified, role in the global carbon cycle. Isotopes provide a fundamental fingerprint of the source of PC and a powerful tracer of interactions between PC and the environment. Radiocarbon and stable carbon isotope techniques have been widely applied to studies of PC in aerosols, soils, sediments and archaeological sequences, with the use of other isotopes currently less developed. This paper reviews the current state of knowledge regarding (i) techniques for isolating PC for isotope analysis and (ii) processes controlling the carbon (<sup>13</sup>C and <sup>14</sup>C), nitrogen, oxygen, hydrogen and sulfur isotope composition of PC during formation and after deposition. It also reviews the current and potential future applications of isotope based studies to better understand the role of PC in the modern environment and to the development of records of past environmental change

Investigations of vegetation and soils information contained in LANDSAT Thematic Mapper and Multispectral Scanner data

An extension of the TM tasseled cap transformation to reflectance factor data is presented, and the basic concepts underlying the tasseled cap transformations are described. The ratio of TM bands 5 and 7, and TM tasseled cap wetness, are both shown to offer promise of direct detection of available soil moisture. Some effects of organic matter and other soil characteristics or constituents on TM tasseled cap spectral response are also considered

HIRIS (High-Resolution Imaging Spectrometer: Science opportunities for the 1990s. Earth observing system. Volume 2C: Instrument panel report

The high-resolution imaging spectrometer (HIRIS) is an Earth Observing System (EOS) sensor developed for high spatial and spectral resolution. It can acquire more information in the 0.4 to 2.5 micrometer spectral region than any other sensor yet envisioned. Its capability for critical sampling at high spatial resolution makes it an ideal complement to the MODIS (moderate-resolution imaging spectrometer) and HMMR (high-resolution multifrequency microwave radiometer), lower resolution sensors designed for repetitive coverage. With HIRIS it is possible to observe transient processes in a multistage remote sensing strategy for Earth observations on a global scale. The objectives, science requirements, and current sensor design of the HIRIS are discussed along with the synergism of the sensor with other EOS instruments and data handling and processing requirements

Influential factors in nectar composition and yield in Leptospermum scoparium : a thesis presented in partial fulfilment of the requirements for the degree of Doctor of Philosophy in Plant Science, Institute of Agriculture and the Environment, College of Sciences, Massey University, Palmerston North, New Zealand

Material omitted from digital version of thesis: Nickless, E. M., Anderson, C. W. N., Hamilton, G., Stephens, J. M., & Wargent, J. (2016). Soil influences on plant growth, floral density and nectar yield in three cultivars of manuka (Leptospermum scoparium). New Zealand Journal of Botany, 55(2), 100-117. doi:10.1080/0028825X.2016.1247732 ; Nickless, E. M., Holroyd, S. E., Stephens, J. M., Gordon, K. C., & Wargent, J. J. (2014). Analytical FT-Raman spectroscopy to chemotype Leptospermum scoparium and generate predictive models for screening for dihydroxyacetone levels in floral nectar. Journal of Raman Spectroscopy, 45(10), 890-894. doi:10.1002/jrs.4576 ; Nickless, E. M., Holroyd, S. E., Hamilton, G., Gordon, K. C., & Wargent, J. J. (2016). Analytical method development using FTIR-ATR and FT-Raman spectroscopy to assay fructose, sucrose, glucose and dihydroxyacetone, in Leptospermum scoparium nectar. Vibrational Spectroscopy, 84 (2016), 38-43. doi:10.1016/j.vibspec.2016.02.011Leptospermum scoparium (Mānuka) is the plant nectar source for medically bioactive honey, commercially marketed in New Zealand as Unique Mānuka Factor honey (UMF-honey). Methylglyoxal (MGO) is the unique bioactive component of UMF honey with Mānuka nectar containing significant amounts of the carbohydrate dihydroxyacetone (DHA), the chemical precursor for MGO. Anecdotal evidence and recently published data from nectar samples collected from various cultivars in natural sites or botanical gardens has indicated that the DHA and overall composition of L. scoparium nectar varies according to cultivar. The source of this variation is not clearly understood and although there is considerable literature on climatic and genetic influences on nectar composition and yield within various other plant species, there is little published work available on the influence of genetic and environmental factors on the composition and yield of nectar in L. scoparium. Of value to the commercial UMF honey industry in New Zealand is the ability to assess cultivars from breeding programs for the best potential to increase overall UMF honey yield. Predictive modelling of yields is invaluable to the developing honey industry to allow assessment of environmental influences that may affect overall yield along with seasonal influences on nectar production in Mānuka. The research in this thesis establishes the effect of various parameters on overall DHA yield from Mānuka and the beginnings of modelling influencing environmental factors. To determine influences on dihydroxyacetone (DHA) concentration and yield in the nectar of L. scoparium a number of studies were carried out. Methodologies for the collection and analysis of nectar were established. Ten different cultivars of L. scoparium with a range of genetic parentage were studied in controlled glasshouse conditions to assess phenotypic variability in terms of nectar composition and yield as well as plant growth and flowering amongst these cultivars. Significant differences in plant growth and flowering habits were observed amongst the ten cultivars, significant differences in nectar yield and nectar composition with regard to DHA yield were also observed. DHA yields ranged from 2714-7459 mg of DHA/kilogram normalised to 80 oBRIX, with total nectar sugar yields ranging between 0.7 and 4.8 mg amongst the ten cultivars studied. Preliminary research into the effect of temperature, radiation and humidity on nectar composition and yield were also undertaken. Effects of soil composition on these same parameters were researched with a subset of three of the ten cultivars grown on ten different soil types. Plant relative growth rates, dry weights and total plant height were measured throughout a 15 month glasshouse trial. Plant growth, flowering phenology, floral density, nectar yield and DHA composition data was gathered. Soils were analysed for various macronutrient and micronutrient levels and these parameters were modelled against plant data to determine which soil components were influencing plant parameters of interest. Soil type was shown to have no significant effect on DHA concentrations in nectar but results did show that soil type had a significant effect on flowering density amongst the three L. scoparium cultivars studied in the trial. Results from regression analysis of soil chemistry against measured plant parameters indicate that a fertiliser regime has the potential to increase nectar yields due to increased flower numbers. Multivariate analysis using partial least squares regression of soil composition data against plant parameters of value showed that soil components; phosphorus, sulphate, ferric and chloride were commonly shown to influence plant parameters measured. Analytical spectroscopy was investigated as a method to chemotype L. scoparium cultivars and also as a method for quantifying nectar components sucrose, glucose, fructose and DHA. Nectar composition was analysed using high pressure liquid chromatography (HPLC) and compared with fourier transform Raman spectroscopy (FT-Raman) and attenuated total reflectance infrared spectroscopy (ATR-FTIR) analytical spectroscopy methods. FT-Raman spectroscopy was shown to be useful in chemotyping cultivars and in addition proved to be a useful analytical method to predict DHA yield using leaf material from L. scoparium plants from the ten cultivars. FT-Raman and ATR-FTIR proved to be relatively accurate techniques to quantify L. scoparium nectar components DHA, fructose, glucose and sucrose, compared with HPLC methods which use extensive preparation techniques. R-squared values were very good for all nectar components measured excepting the sucrose model at R2 = 0.77. The R2 for the FT-Raman predictions of DHA against HPLC data are very good at 0.85. FTIR prediction data against HPLC data was also good at 0.86 R2. Overall an accurate model is possible for quantifying DHA concentrations in nectar using both FTIR-ATR and FT-Raman spectroscopy. Overall results show that various factors need to be considered when assessing plants for commercial use in the (UMF) Mānuka honey industry within New Zealand. Due to their large impact on overall nectar yield; floral density and plant growth rate parameters are the two key factors of value for commercial assessment of Mānuka cultivars. This research also highlights the importance of assessing not just DHA concentration in deducing cultivar value, but overall nectar yield. These key features must be explored when assessing L. scoparium plants within breeding programs, prior to selection for large-scale field production of high UMF Mānuka honey