Automating Crop Damage Assessments with Unmanned Aerial Systems and Machine Learning

Agricultural pests are responsible for millions of dollars in crop losses and management costs every year. In order to implement optimal site-specific treatments and reduce control costs, new methods to accurately monitor and assess pest damage need to be investigated. In this paper we explore the combination of unmanned aerial vehicles (UAV), remote sensing and machine learning techniques as a promising methodology to address this challenge. The deployment of UAVs as a sensor platform is a rapidly growing field of study for biosecurity and precision agriculture applications. In this experiment, a data collection campaign is performed over a sorghum crop severely damaged by white grubs (Coleoptera: Scarabaeidae). The larvae of these scarab beetles feed on the roots of plants, which in turn impairs root exploration of the soil profile. In the field, crop health status could be classified according to three levels: bare soil where plants were decimated, transition zones of reduced plant density and healthy canopy areas. In this study, we describe the UAV platform deployed to collect high-resolution RGB imagery as well as the image processing pipeline implemented to create an orthoimage. An unsupervised machine learning approach is formulated in order to create a meaningful partition of the image into each of the crop levels. The aim of this approach is to simplify the image analysis step by minimizing user input requirements and avoiding the manual data labelling necessary in supervised learning approaches. The implemented algorithm is based on the K-means clustering algorithm. In order to control high-frequency components present in the feature space, a neighbourhood-oriented parameter is introduced by applying Gaussian convolution kernels prior to K-means clustering. The results show the algorithm delivers consistent decision boundaries that classify the field into three clusters, one for each crop health level as shown in Figure 1. The methodology presented in this paper represents a venue for further esearch towards automated crop damage assessments and biosecurity surveillance.

Characterization of disease resistance gene candidates of the nucleotide binding site (NBS) type from banana and correlation of a transcriptional polymorphism with resistance to Fusarium oxysporum f.sp. cubense race 4

Most plant disease resistance (R) genes encode proteins with a nucleotide binding site and leucine-rich repeat structure (NBS-LRR). In this study, degenerate primers were used to amplify genomic NBS-type sequences from wild banana (Musa acuminata ssp. malaccensis) plants resistant to the fungal pathogen Fusarium oxysporum formae specialis (f. sp.) cubense (FOC) race 4. Five different classes of NBS-type sequences were identified and designated as resistance gene candidates (RGCs). The deduced amino acid sequences of the RGCs revealed the presence of motifs characteristic of the majority of known plant NBS-LRR resistance genes. Structural and phylogenetic analyses grouped the banana RGCs within the non-TIR (homology to Toll/interleukin-1 receptors) subclass of NBS sequences. Southern hybridization showed that each banana RGC is present in low copy number. The expression of the RGCs was assessed by RT-PCR in leaf and root tissues of plants resistant or susceptible to FOC race 4. RGC1, 3 and 5 showed a constitutive expression profile in both resistant and susceptible plants whereas no expression was detected for RGC4. Interestingly, RGC2 expression was found to be associated only to FOC race 4 resistant lines. This finding could assist in the identification of a FOC race 4 resistance gene.

Availability of soil potassium and diagnostic soil tests

Thirty-seven surface (0-0.10 or 0-0.20 m) soils covering a wide range of soil types (16 Vertosols, 6 Ferrosols, 6 Dermosols, 4 Hydrosols, 2 Kandosols, 1 Sodosol, 1 Rudosol, and 1 Chromosol) were exhaustively cropped in 2 glasshouse experiments. The test species were Panicum maximum cv. Green Panic in Experiment A and Avena sativa cv. Barcoo in Experiment B. Successive forage harvests were taken until the plants could no longer grow in most soils because of severe potassium (K) deficiency. Soil samples were taken prior to cropping and after the final harvest in both experiments, and also after the initial harvest in Experiment B. Samples were analysed for solution K, exchangeable K (Exch K), tetraphenyl borate extractable K for extraction periods of 15 min (TBK15) and 60 min (TBK60), and boiling nitric acid extractable K (Nitric K). Inter-correlations between the initial levels of the various soil K parameters indicated that the following pools were in sequential equilibrium: solution K, Exch K, fast release fixed K [estimated as (TBK15-Exch K)], and slow release fixed K [estimated as (TBK60-TBK15)]. Structural K [estimated as (Nitric K-TBK60)] was not correlated with any of the other pools. However, following exhaustive drawdown of soil K by cropping, structural K became correlated with solution K, suggesting dissolution of K minerals when solution K was low. The change in the various K pools following cropping was correlated with K uptake at Harvest 1 ( Experiment B only) and cumulative K uptake ( both experiments). The change in Exch K for 30 soils was linearly related to cumulative K uptake (r = 0.98), although on average, K uptake was 35% higher than the change in Exch K. For the remaining 7 soils, K uptake considerably exceeded the change in Exch K. However, the changes in TBK15 and TBK60 were both highly linearly correlated with K uptake across all soils (r = 0.95 and 0.98, respectively). The slopes of the regression lines were not significantly different from unity, and the y-axis intercepts were very small. These results indicate that the plant is removing K from the TBK pool. Although the change in Exch K did not consistently equate with K uptake across all soils, initial Exch K was highly correlated with K uptake (r = 0.99) if one Vertosol was omitted. Exchangeable K is therefore a satisfactory diagnostic indicator of soil K status for the current crop. However, the change in Exch K following K uptake is soil-dependent, and many soils with large amounts of TBK relative to Exch K were able to buffer changes in Exch K. These soils tended to be Vertosols occurring on floodplains. In contrast, 5 soils (a Dermosol, a Rudosol, a Kandosol, and 2 Hydrosols) with large amounts of TBK did not buffer decreases in Exch K caused by K uptake, indicating that the TBK pool in these soils was unavailable to plants under the conditions of these experiments. It is likely that K fertiliser recommendations will need to take account of whether the soil has TBK reserves, and the availability of these reserves, when deciding rates required to raise exchangeable K status to adequate levels.

Soil properties and crop yields in a dryland Vertisol sown with cotton-based crop rotations

Information on the effects of growing cotton (Gossypium hirsutum L.)-based crop rotations on soil quality of dryland Vertisols is sparse. The objective of this study was to quantify the effects of growing cereal and leguminous crops in rotation with dryland cotton on physical and chemical properties of a grey Vertisol near Warra, SE Queensland, Australia. The experimental treatments, selected after consultations with local cotton growers, were continuous cotton (T1), cotton-sorghum (Sorghum bicolor (L.) Moench.) (T2), cotton-wheat (Triticum aestivum L.) double cropped (T3), cotton-chickpea (Cicer arietinum L.) double cropped followed by wheat (T4) and cotton-wheat (T5). From 1993 to 1996 land preparation was by chisel ploughing to about 0.2 m followed by two to four cultivations with a Gyral tyne cultivator. Thereafter all crops were sown with zero tillage except for cultivation with a chisel plough to about 0.07-0.1 m after cotton picking to control heliothis moth pupae. Soil was sampled from 1996 to 2004 and physical (air-filled porosity of oven-dried soil, an indicator of soil compaction; plastic limit; linear shrinkage; dispersion index) and chemical (pH in 0.01 M CaCl2, organic carbon, exchangeable Ca, Mg, K and Na contents) properties measured. Crop rotation affected soil properties only with respect to exchangeable Na content and air-filled porosity. In the surface 0.15 m during 2000 and 2001 lowest air-filled porosity occurred with T1 (average of 34.6 m3/100 m3) and the highest with T3 (average of 38.9 m3/100 m3). Air-filled porosity decreased in the same depth between 1997 and 1998 from 45.0 to 36.1 m3/100 m3, presumably due to smearing and compaction caused by shallow cultivation in wet soil. In the subsoil, T1 and T2 frequently had lower air-filled porosity values in comparison with T3, T4 and T5, particularly during the early stages of the experiment, although values under T1 increased subsequently. In general, compaction was less under rotations which included a wheat crop (T3, T4, T5). For example, average air-filled porosity (in m3/100 m3) in the 0.15-0.30 m depth from 1996 to 1999 was 19.8 with both T1 and T2, and 21.2 with T3, 21.1 with T4 and 21.5 with T5. From 2000 to 2004, average air-filled porosity (in m3/100 m3) in the same depth was 21.3 with T1, 19.0 with T2, 19.8 with T3, 20.0 with T4 and 20.5 with T5. The rotation which included chickpea (T4) resulted in the lowest exchangeable Na content, although differences among rotations were small. Where only a cereal crop with a fibrous root system was sown in rotation with cotton (T2, T3, T5) linear shrinkage in the 0.45-0.60 m depth was lower than in rotations, which included tap-rooted crops such as chickpea (T4) or continuous cotton (T1). Dispersion index and organic carbon decreased, and plastic limit increased with time. Soil organic carbon stocks decreased at a rate of 1.2 Mg/ha/year. Lowest average cotton lint yield occurred with T2 (0.54 Mg/ha) and highest wheat yield with T3 (2.8 Mg/ha). Rotations which include a wheat crop are more likely to result in better soil structure and cotton lint yield than cotton-sorghum or continuous cotton.

Application of phytotoxicity data to a new Australian soil quality guideline framework for biosolids

To protect terrestrial ecosystems and humans from contaminants many countries and jurisdictions have developed soil quality guidelines (SQGs). This study proposes a new framework to derive SQGs and guidelines for amended soils and uses a case study based on phytotoxicity data of copper (Cu) and zinc (Zn) from field studies to illustrate how the framework could be applied. The proposed framework uses normalisation relationships to account for the effects of soil properties on toxicity data followed by a species sensitivity distribution (SSD) method to calculate a soil added contaminant limit (soil ACL) for a standard soil. The normalisation equations are then used to calculate soil ACLs for other soils. A soil amendment availability factor (SAAF) is then calculated as the toxicity and bioavailability of pure contaminants and contaminants in amendments can be different. The SAAF is used to modify soil ACLs to ACLs for amended soils. The framework was then used to calculate soil ACLs for copper (Cu) and zinc (Zn). For soils with pH of 4-8 and OC content of 1-6%, the ACLs range from 8 mg/kg to 970 mg/kg added Cu. The SAAF for Cu was pH dependant and varied from 1.44 at pH 4 to 2.15 at pH 8. For soils with pH of 4-8 and OC content of 1-6%, the ACLs for amended soils range from 11 mg/kg to 2080 mg/kg added Cu. For soils with pH of 4-8 and a CEC from 5-60, the ACLs for Zn ranged from 21 to 1470 mg/kg added Zn. A SAAF of one was used for Zn as it concentrations in plant tissue and soil to water partitioning showed no difference between biosolids and soluble Zn salt treatments, indicating that Zn from biosolids and Zn salts are equally bioavailable to plants.

Rice responses to soil management in a rice-based cropping system in the semi-arid tropics of southern Lombok, Eastern Indonesia

This paper is the first of a series that investigates whether new cropping systems with permanent raised beds (PRBs) or Flat land could be successfully used to increase farmers' incomes from rainfed crops in Lombok in Eastern Indonesia. This paper discusses the rice phase of the cropping system. Low grain yields of dry-seeded rice (Oryza sativa) grown on Flat land on Vertisols in the rainfed region of southern Lombok, Eastern Indonesia, are probably mainly due to (a) erratic rainfall (870-1220 mm/yr), with water often limiting at sensitive growth stages, (b) consistently high temperatures (average maximum - 31 C), and (c) low solar radiation. Farmers are therefore poor, and labour is hard and costly, as all operations are manual. Two replicated field experiments were run at Wakan (annual rainfall = 868 mm) and Kawo (1215 mm) for 3 years (2001/2002 to 2003/2004) on Vertisols in southern Lombok. Dry-seeded rice was grown in 4 treatments with or without manual tillage on (a) PRBs, 1.2 m wide, 200 mm high, separated by furrows 300 mm wide, 200 mill deep, with no rice sown in the well-graded furrows, and (b) well-graded Flat land. Excess surface water was harvested from each treatment and used for irrigation after the vegetative stage of the rice. All operations were manual. There were no differences between treatments in grain yield of rice (mean grain yield = 681 g/m(2)) which could be partly explained by total number of tillers/hill and mean panicle length, but not number of productive tillers/hill, plant height or weight of 1000 grains. When the data from both treatments on PRBs and from both treatments on Flat land, each year at each site were analysed, there were also no differences in grain yield of rice (g/m(2)). When rainfall in the wet season up to harvest was over 1000 mm (Year 2; Wakan, Kawo), or plants were water-stressed during crop establishment (Year 1; Wakan) or during grain-fill (Year 3: Kawo), there were significant differences in grain yield (g/1.5 m(2)) between treatments; generally the grain yield (g/1.5 m(2)) on PRBs with or without tillage was less than that on Flat land with or without tillage. However, when the data from both treatments on PRBs and from both treatments on Flat land, each year at each site, were analysed, the greater grain yield of dry-seeded rice on Flat land (mean yield 1 092 g/1.5 m(2)) than that on PRBs (mean 815 g/1.5 m(2)) was mainly because there were 25% more plants on Flat land. Overall when the data in the 2 outer rows and the 2 inner rows on PRBs were each combined, there was a higher number of productive tillers in the combined outer rows (mean 20.7 tillers/hill) compared with that in the combined inner rows on each PRB (mean 18.2 tillers/hill). However, there were no differences in grain yield between combined rows (mean 142 g/m row). Hence with a gap of 500 mm (the distance between the outer rows of plants on adjacent raised beds), plants did not compensate in grain yield for missing plants in furrows. This suggests that rice (a) also sown in furrows, or (b) sown in 7 rows with narrower row-spacing, or (c) sown in 6 rows with slightly wider row-spacing, and narrower gap between outer rows on adjacent beds, may further increase grain yield (g/1.5 m(2)) in this system of PRBs. The growth and the grain yield (y in g/m(2)) of rainfed rice (with rainfall on-site the only source of water for irrigation) depended mainly on the rainfall (x in mm) in the wet season up to harvest (due either to site or year) with y = 1. 1x -308; r(2) = 0.54; p < 0.005. However, 280 mm (i.e. 32%) of the rainfall was not directly used to produce grain (i.e. when y = 0 g/m(2)). Manual tillage did not affect growth and grain yield of rice (g/m(2); g/1.5 m(2)), either on PRB or on Flat land.

Row spacing and planting density effects on the growth and yield of sugarcane. 1. Responses in fumigated and non-fumigated soil.

It has been reported that high-density planting of sugarcane can improve cane and sugar yield through promoting rapid canopy closure and increasing radiation interception earlier in crop growth. It is widely known that the control of adverse soil biota through fumigation (removes soil biological constraints and improves soil health) can improve cane and sugar yield. Whether the responses to high-density planting and improved soil health are additive or interactive has important implications for the sugarcane production system. Field experiments established at Bundaberg and Mackay, Queensland, Australia, involved all combinations of 2-row spacings (0.5 and 1.5 m), two planting densities (27 000 and 81 000 two-eyed setts/ha), and two soil fumigation treatments (fumigated and non-fumigated). The Bundaberg experiment had two cultivars (Q124, Q155), was fully irrigated, and harvested 15 months after planting. The Mackay experiment had one cultivar (Q117), was grown under rainfed conditions, and harvested 10 months after planting. High-density planting (81 000 setts/ha in 0.5-m rows) did not produce any more cane or sugar yield at harvest than low-density planting (27 000 setts/ha in 1.5-m rows) regardless of location, crop duration (15 v. 10 months), water supply (irrigated v. rainfed), or soil health (fumigated v. non-fumigated). Conversely, soil fumigation generally increased cane and sugar yields regardless of site, row spacing, and planting density. In the Bundaberg experiment there was a large fumigation x cultivar x density interaction (P<0.01). Cultivar Q155 responded positively to higher planting density in non-fumigated soil but not in fumigated soil, while Q124 showed a negative response to higher planting density in non-fumigated soil but no response in fumigated soil. In the Mackay experiment, Q117 showed a non-significant trend of increasing yield in response to increasing planting density in non-fumigated soil, similar to the Q155 response in non-fumigated soil at Bundaberg. The similarity in yield across the range of row spacings and planting densities within experiments was largely due to compensation between stalk number and stalk weight, particularly when fumigation was used to address soil health. Further, the different cultivars (Q124 and Q155 at Bundaberg and Q117 at Mackay) exhibited differing physiological responses to the fumigation, row spacing, and planting density treatments. These included the rate of tiller initiation and subsequent loss, changes in stalk weight, and propensity to lodging. These responses suggest that there may be potential for selecting cultivars suited to different planting configurations.

Soil type does not affect seed ageing when soil water potential and temperature are controlled

To investigate the effects of soil type on seed persistence in a manner that controlled for location and climate variables, three weed species—Gomphocarpus physocarpus (swan plant), Avena sterilis ssp. ludoviciana (wild oat) and Ligustrum lucidum (broadleaf privet)—were buried for 21 months in three contrasting soils at a single location. Soil type had a significant effect on seed persistence and seedling vigour, but soil water content and temperature varied between soils due to differences in physical and chemical properties. Warmer, wetter conditions favoured shorter persistence. A laboratory-based test was developed to accelerate the rate of seed ageing within soils, using controlled superoptimal temperature and moisture conditions (the soil-specific accelerated ageing test, SSAAT). The SSAAT demonstrated that soil type per se did not influence seed longevity. Moreover, the order in which seeds aged was the same whether aged in the field or SSAAT, with L. lucidum being shortest-lived and A. sterilis being longest-lived of the three species.

Lantana camara L. (Verbenaceae) invasion effects on soil physicochemical properties

Lantana camara is a recognized weed of worldwide significance due to its extensive distribution and its impacts on primary industries and nature conservation. However, quantitative data on the impact of the weed on soil ecosystem properties are scanty, especially in SE Australia, despite the pervasive presence of the weed along its coastal and inland regions. Consequently, mineral soils for physicochemical analyses were collected beneath and away from L. camara infestations in four sites west of Brisbane, SE Australia. These sites (hoop pine plantation, cattle farm, and two eucalyptus forests with occasional grazing and a fire regime, respectively) vary in landscape and land-use types. Significant site effect was more frequently observed than effect due to invasion status. Nonetheless, after controlling for site differences, ~50% of the 23 soil traits examined differed significantly between infested and non-infested soils. Moisture, pH, Ca, total and organic C, and total N (but not exchangeable N in form of NO3-) were significantly elevated, while sodium, chloride, copper, iron, sulfur, and manganese, many of which can be toxic to plant growth if present in excess levels, were present at lower levels in soils supporting L. camara compared to soils lacking the weed. These results indicate that L. camara can improve soil fertility and influence nutrient cycling, making the substratum ideal for its own growth and might explain the ability of the weed to outcompete other species, especially native ones.

Quantifying surfactant interaction effects on soil moisture

Quantifying surfactant interaction effects on soil moisture and turf quality.

Defining critical soil nutrient concentrations in soils supporting grains and cotton in Northern NSW and Queensland

This project focussed on the phosphorus (P) and potassium (K) status of northern cropping soils. Stores of P and K have been depleted by crop removal and limited fertiliser application, with depletion most significant in the subsoil. Soil testing strategies are confounded by slowly available mineral reserves with uncertain availability. The utility of new soil tests was assessed to measure these reserves, their availability to plants quantified and a regional sampling strategy undertaken to identify areas of greatest P and K deficit. Fertiliser application strategies for P and K have been tested and the interactions between these and other nutrients have been determined in a large field program.

Soil C stocks in grains and sugar farming systems

Quantify soil C stocks in grains and sugarcane cropping systems of Queensland, including impacts of management practices.

Innovative management of herbicide resistant weeds - seed banks and soil biology

The project will evaluate seed bank depletion of key northern herbicide resistant weeds under different environments, cropping systems, crop agronomies and non-chemical control tactics. The project will also evaluate soil biology and seed bank relationships to explain differences in seed bank persistence.

Influence of soil organic amendments on suppression of the burrowing nematode, Radopholus similis, on the growth of bananas.

Radopholus similis is a major constraint to banana production in Australia and growers have relied on nematicides to manage production losses. The use of organic amendments is one method that may reduce the need for nematicides, but there is limited knowledge of the influence of organic amendments on endo-migratory nematodes, such as R. similis. Nine different amendments, namely, mill mud, mill ash, biosolids, municipal waste compost, banana residue, grass hay, legume hay, molasses and calcium silicate were applied to the three major soil types of the wet tropics region used for banana production. The nutrient content of the amendments was also determined. Banana plants were inoculated with R. similis and grown in the soil-amendment mix for 12-weeks in a glasshouse experiment. Assessments of plant growth, plant-parasitic nematodes and soil nematode community characteristics were made at the termination of the experiment. Significant suppression of plant-parasitic nematodes occurred in soils amended with legume hay, grass hay, banana residue and mill mud relative to untreated soil. These amendments were found to have the highest N and C content. The application of banana residue and mill mud significantly increased shoot dry weight at the termination of the experiment relative to untreated soil. Furthermore, the applications of banana residue, grass hay, mill mud and municipal waste compost increased the potential for suppression of plant-parasitic nematodes through antagonistic activity. The application of amendments that are high in C and N appeared to be able to induce suppression of plant-parasitic nematodes in bananas, by developing a more favourable environment for antagonistic organisms.

Cat's claw creeper vine, Macfadyena unguis-cati (Bignoniaceae), invasion impacts: comparative leaf nutrient content and effects on soil physicochemical properties

Macfadyena unguis-cati (L.) Gentry (Bignoniaceae) is a major environmental weed in coastal Queensland, Australia. There is a lack of quantitative data on its leaf chemistry and its impact on soil properties. Soils from infested vs uninfested areas, and leaves of M. unguis-cati and three co-occurring vine species (one exotic, two native) were collected at six sites (riparian and non-riparian) in south-eastern Queensland. Effects of invasion status, species, site and habitat type were examined using univariate and multivariate analyses. Habitat type had a greater effect on soil nutrients than on leaf chemistry. Invasion effect of M. unguis-cati on soil chemistry was more pronounced in non-riparian than in riparian habitat. Significantly higher values were obtained in M. unguis-cati infested (vs. uninfested) soils for ~50% of traits. Leaf ion concentrations differed significantly between exotic and native vines. Observed higher leaf-nutrient load (especially nitrogen, phosphorus and potassium) in exotic plants aligns with the preference of invasive plant species for disturbed habitats with higher nutrient input. Higher load of trace elements (aluminium, boron, cadmium and iron) in its leaves suggests that cycling of heavy-metal ions, many of which are potentially toxic at excess level, could be accelerated in soils of M. unguis-cati-invaded landscape. Although inferences from the present study are based on correlative data, the consistency of the patterns across many sites suggests that M. unguis-cati may improve soil fertility and influence nutrient cycling, perhaps through legacy effects of its own litter input.