Lynne M. Macdonald

The Performance of Visible, Near-, and Mid-Infrared Reflectance Spectroscopy for Prediction of Soil Physical, Chemical, and Biological Properties

Abstract This review addresses the applicability of visible (Vis), near-infrared (NIR), and mid-infrared (MIR) reflectance spectroscopy for the prediction of soil properties. We address (1) the properties that can be predicted and the accuracy of the predictions, (2) the most suitable spectral regions for specific soil properties, (3) the number of predictions reported for each property, and (4) in-field versus laboratory spectral techniques. We found the following properties to be successfully predicted: soil water content, texture, soil carbon (C), cation exchange capacity, calcium and magnesium (exchangeable), total nitrogen (N), pH, concentration of metals/metalloids, microbial size, and activity. Generally, MIR produced better predictions than Vis-NIR, but Vis-NIR outperformed MIR for a number of properties (e.g., biological). An advantage of Vis-NIR is instrument portability although a new range of MIR portable devices is becoming available. In-field predictions for clay, water, total organic C, extractable phosphorus, total C and N appear similar to laboratory methods, but there are issues regarding, for example, sample heterogeneity, moisture content, and surface roughness. The nature of the variable being predicted, the quality and consistency of the reference laboratory methods, and the adequate representation of unknowns by the calibration set must be considered when predicting soil properties using reflectance spectroscopy.

Microbial utilisation Of biochar-derived carbon

Whilst largely considered an inert material, biochar has been documented to contain a small yet significant fraction of microbially available labile organic carbon (C). Biochar addition to soil has also been reported to alter soil microbial community structure, and to both stimulate and retard the decomposition of native soil organic matter (SOM). We conducted a short-term incubation experiment using two (13)C-labelled biochars produced from wheat or eucalypt shoots, which were incorporated in an aridic arenosol to examine the fate of the labile fraction of biochar-C through the microbial community. This was achieved using compound specific isotopic analysis (CSIA) of phospholipid fatty acids (PLFAs). A proportion of the biologically-available fraction of both biochars was rapidly (within three days) utilised by gram positive bacteria. There was a sharp peak in CO2 evolution shortly after biochar addition, resulting from rapid turnover of labile C components in biochars and through positive priming of native SOM. Our results demonstrate that this CO2 evolution was at least partially microbially mediated, and that biochar application to soil can cause significant and rapid changes in the soil microbial community; likely due to addition of labile C and increases in soil pH.

Predicting contents of carbon and its component fractions in Australian soils from diffuse reflectance mid-infrared spectra

Quantifying the content and composition of soil carbon in the laboratory is time-consuming, requires specialised equipment and is therefore expensive. Rapid, simple and low-cost accurate methods of analysis are required to support current interests in carbon accounting. This study was completed to develop national and state-based models capable of predicting soil carbon content and composition by coupling diffuse reflectance mid-infrared (MIR) spectra with partial least-squares regression (PLSR) analyses. Total, organic and inorganic carbon contents were determined and MIR spectra acquired for 20 495 soil samples collected from 4526 locations from soil depths to 1 m within Australia’s agricultural regions. However, all subsequent MIR/PLSR models were developed using soils only collected from the 0–10, 10–20 and 20–30 cm depth layers. The extent of grinding applied to air-dried soil samples was found to be an important determinant of the variability in acquired MIR spectra. After standardisation of the grinding time, national MIR/PLSR models were developed using an independent test-set validation approach to predict the square-root transformed contents of total, organic and inorganic carbon and total nitrogen. Laboratory fractionation of soil organic carbon into particulate, humus and resistant forms was completed on 312 soil samples. Reliable national MIR/PLSR models were developed using cross-validation to predict the contents of these soil organic carbon fractions; however, further work is required to enhance the representation of soils with significant contents of inorganic carbon. Regional MIR/PLSR models developed for total, organic and inorganic carbon and total nitrogen contents were found to produce more reliable and accurate predictions than the national models. The MIR/PLSR approach offers a more rapid and more cost effective method, relative to traditional laboratory methods, to derive estimates of the content and composition of soil carbon and total nitrogen content provided that the soils are well represented by the calibration samples used to build the predictive models.

Quantifying the allocation of soil organic carbon to biologically significant fractions

Soil organic carbon (OC) exists as a diverse mixture of organic materials with different susceptibilities to biological decomposition. Computer simulation models constructed to predict the dynamics of soil OC have dealt with this diversity using a series of conceptual pools differentiated from one another by the magnitude of their respective decomposition rate constants. Research has now shown that the conceptual pools can be replaced by measureable fractions of soil OC separated on the basis of physical and chemical properties. In this study, an automated protocol for allocating soil OC to coarse (>50 µm) and fine (≤50 µm) fractions was assessed. Automating the size fractionation process was shown to reduce operator dependence and variability between replicate analyses. Solid-state 13C nuclear magnetic resonance spectroscopy was used to quantify the content of biologically resistant poly-aryl carbon in the coarse and fine size fractions. Cross-polarisation analyses were completed for coarse and fine fractions of 312 soils, and direct polarisation analyses were completed for 38 representative fractions. Direct polarisation analyses indicated that the resistant poly-aryl carbon was under-represented in the cross-polarisation analyses, on average, by a factor of ~2. Combining this under-representation with a spectral analysis process allowed the proportion of coarse- and fine-fraction OC existing as resistant poly-aryl C to be defined. The content of resistant OC was calculated as the sum of that found in the coarse and fine fractions. Contents of particulate and humus OC were calculated after subtracting the resistant OC from the coarse and fine fractions, respectively. Across the 312 soils analysed, substantial variations in the contents of humus, particulate, and resistant carbon were noted, with respective average values of 9.4, 4.0, and 4.5 g fraction C/kg soil obtained. When expressed as a proportion of the OC present in each soil, the humus, particulate, and resistant OC accounted for 56, 19, and 26%, respectively. The nuclear magnetic resonance analyses also indicated that the use of a 50-µm sieve to differentiate particulate (>50 µm) from humus (≤50 µm) forms of OC provided an effective separation based on extents of decomposition. The procedures developed in this study provided a means to differentiate three biologically significant forms of soil OC based on size, extent of decomposition, and chemical composition (poly-aryl content).

Poor efficacy of herbicides in biochar-amended soils as affected by their chemistry and mode of action

We evaluated wheat straw biochar produced at 450°C for its ability to influence bioavailability and persistence of two commonly used herbicides (atrazine and trifluralin) with different modes of action (photosynthesis versus root tip mitosis inhibitors) in two contrasting soils. The biochar was added to soils at 0%, 0.5% and 1.0% (w/w) and the herbicides were applied to those soil-biochar mixes at nil, half, full, two times, and four times, the recommended dosage (H(4)). Annual ryegrass (Lolium rigidum) was grown in biochar amended soils for 1 month. Biochar had a positive impact on ryegrass survival rate and above-ground biomass at most of the application rates, and particularly at H(4). Within any given biochar treatment, increasing herbicide application decreased the survival rate and fresh weight of above-ground biomass. Biomass production across the biochar treatment gradient significantly differed (p<0.01) and was more pronounced in the case of atrazine than trifluralin. For example, the dose-response analysis showed that in the presence of 1% biochar in soil, the value of GR(50) (i.e. the dose required to reduce weed biomass by 50%) for atrazine increased by 3.5 times, whereas it increased only by a factor of 1.6 in the case of trifluralin. The combination of the chemical properties and the mode of action governed the extent of biochar-induced reduction in bioavailability of herbicides. The greater biomass of ryegrass in the soil containing the highest biochar (despite having the highest herbicide residues) demonstrates decreased bioavailability of the chemicals caused by the wheat straw biochar. This work clearly demonstrates decreased efficacy of herbicides in biochar amended soils. The role played by herbicide chemistry and mode of action will have major implications in choosing the appropriate application rates for biochar amended soils.

Network analysis reveals that bacteria and fungi form modules that correlate independently with soil parameters

Network and multivariate statistical analyses were performed to determine interactions between bacterial and fungal community terminal restriction length polymorphisms as well as soil properties in paired woodland and pasture sites. Canonical correspondence analysis (CCA) revealed that shifts in woodland community composition correlated with soil dissolved organic carbon, while changes in pasture community composition correlated with moisture, nitrogen and phosphorus. Weighted correlation network analysis detected two distinct microbial modules per land use. Bacterial and fungal ribotypes did not group separately, rather all modules comprised of both bacterial and fungal ribotypes. Woodland modules had a similar fungal : bacterial ribotype ratio, while in the pasture, one module was fungal dominated. There was no correspondence between pasture and woodland modules in their ribotype composition. The modules had different relationships to soil variables, and these contrasts were not detected without the use of network analysis. This study demonstrated that fungi and bacteria, components of the soil microbial communities usually treated as separate functional groups as in a CCA approach, were co-correlated and formed distinct associations in these adjacent habitats. Understanding these distinct modular associations may shed more light on their niche space in the soil environment, and allow a more realistic description of soil microbial ecology and function.

In Situ Persistence and Migration of Biochar Carbon and Its Impact on Native Carbon Emission in Contrasting Soils under Managed Temperate Pastures

Pyrogenic carbon (PyC) is an important component of the global soil carbon (C) pool, but its fate, persistence, and loss dynamics in contrasting soils and environments under planted field conditions are poorly understood. To fill this knowledge gap, a 13C-labelled biochar, as a surrogate material for PyC, produced from Eucalyptus saligna by slow pyrolysis (450°C; δ13C -36.7‰) was surface (0−10 cm) applied in C3 dominated temperate pasture systems across Arenosol, Cambisol and Ferralsol. The results show a low proportion of the applied biochar-C mineralised over 12 months in a relatively clay- and C-poor Arenosol (i.e., 2.0% loss via mineralisation), followed by a clay- and C-rich Cambisol (4.6%), and clay-, C- and earthworm-rich Ferralsol (7.0%). The biochar-C mean residence time (MRT), estimated by different models, varied between 44−1079 (Arenosol), 18−172 (Cambisol), and 11−29 (Ferralsol) years, with the shorter MRT estimated by a one-pool exponential and the longer MRT by an infinite-pool power or a two-pool exponential model. The two-pool model was best fitted to biochar-C mineralisation. The biochar-C recovery in the 12−30 cm soil layer varied from between 1.2% (Arenosol), 2.5−2.7% (Cambisol) and 13.8−15.7% (Ferralsol) of the applied biochar-C after 8−12 months. There was a further migration of biochar-C below the 50-cm depth in the Arenosol, as the combined biochar-C recovery in the mineralised pool and soil profile (up to 30 or 50 cm) was 82%, in contrast to 101% in the Cambisol and 104% in the Ferralsol after 12 months. These results indicate that the downward migration of biochar-C was greatest in the Arenosol (cf. Cambisol and Ferralsol). Cumulative CO2-C emission from native soil-plant sources was lower (p <0.10) in the biochar-amended vs. non-amended Ferralsol. This field-based study shows that the downward migration of biochar-C exceeded its loss via mineralisation in the Arenosol and Ferralsol, but not in the Cambisol. It is thus important to understand biochar-soil interactions to maximise long-term biochar C sequestration potential in planted soil systems.

Opportunities and constraints for biochar technology in Australian agriculture: looking beyond carbon sequestration

The application of biochar technology for soil amendment is largely based on evidence about soil fertility and crop productivity gains made in the Amazonian Black Earth (terra preta). However, the uncertainty of production gains at realistic application rates of biochars and lack of knowledge about other benefits and other concerns may have resulted in poor uptake of biochar technology in Australia so far. In this review, we identify important opportunities as well as challenges in the adoption of biochar technology for broadacre farming and other sectors in Australia. The paper highlights that for biochar technology to be cost-effective and successful, we need to look beyond carbon sequestration and explore other opportunities to value-add to biochar. Therefore, some emerging and novel applications of biochar are identified. We also suggest some priority research areas that need immediate attention in order to realise the full potential of biochar technology in agriculture and other sectors in Australia.

Carbon sequestration under subtropical perennial pastures I: Overall trends

The use of subtropical perennial grasses in temperate grazing systems is increasingly being promoted for production and environmental benefits. This study employed a combination of elemental and stable isotope analyses to explore whether pastures sown to either kikuyu (Pennisetum clandestinum) or a combination of panic (Panicum maximum) and Rhodes grass (Chloris gayana) could increase soil organic carbon (SOC) levels in five regions across southern Australia. Carbon was sequestered under kikuyu at a rate of 0.90 ± 0.25 Mg C ha–1 year–1 along the south coast of Western Australia. Lower but still significant sequestration rates were found for kikuyu in South Australia (0.26 ± 0.13 Mg C ha–1 year–1). No changes in SOC were found for panic–Rhodes grass pasture systems in the northern district of Western Australia. Additionally, we found no changes in SOC when kikuyu-based pastures were established on formerly cropped paddocks in the Namoi Catchment of New South Wales. Stable isotope results corroborated these findings and suggested that, where SOC has accumulated, the gains have been dominated by SOC derived from the perennial vegetation and have been concentrated in the upper 10 cm of soil.

Predicting the origin of soil evidence: High throughput eukaryote sequencing and MIR spectroscopy applied to a crime scene scenario.

Soil can serve as powerful trace evidence in forensic casework, because it is highly individualistic and can be characterised using a number of techniques. Complex soil matrixes can support a vast number of organisms that can provide a site-specific signal for use in forensic soil discrimination. Previous DNA fingerprinting techniques rely on variations in fragment length to distinguish between soil profiles and focus solely on microbial communities. However, the recent development of high throughput sequencing (HTS) has the potential to provide a more detailed picture of the soil community by accessing non-culturable microorganisms and by identifying specific bacteria, fungi, and plants within soil. To demonstrate the application of HTS to forensic soil analysis, 18S ribosomal RNA profiles of six forensic mock crime scene samples were compared to those collected from seven reference locations across South Australia. Our results demonstrate the utility of non-bacterial DNA to discriminate between different sites, and were able to link a soil to a particular location. In addition, HTS complemented traditional Mid Infrared (MIR) spectroscopy soil profiling, but was able to provide statistically stronger discriminatory power at a finer scale. Through the design of an experimental case scenario, we highlight the considerations and potential limitations of this method in forensic casework. We show that HTS analysis of soil eukaryotes was robust to environmental variation, e.g. rainfall and temperature, transfer effects, storage effects and spatial variation. In addition, this study utilises novel analytical methodologies to interpret results for investigative purposes and provides prediction statistics to support soil DNA analysis for evidential stages of a case.