Plantation crops

Plantation horticulture is an important part of the economic landscape of many tropical countries. Plantations were developed in association with colonial expansion and the original models were based on the production of monocrops which had a ready export market, using cheap or slave labour. Plantations in the twenty first Century are less likely environments for exploitation of human and environmental capital. They are however, linked to crop production on a large scale for produce to be sold, at profit, for export to distant markets rather than local sale. A range of crops can be broadly categorized into plantation crops. Plantations continue to be effective models for efficient agricultural production and will evolve in response to the continued demand for food, fruit, fibre, oil crops and timber from a growing population

Evaluation of potential candidate genes involved in salinity tolerance in striped catfish (Pangasianodon hypophthalmus) using an RNA-Seq approach

Increasing salinity levels in freshwater and coastal environments caused by sea level rise linked to climate change is now recognized to be a major factor that can impact fish growth negatively, especially for freshwater teleost species. Striped catfish (Pangasianodon hypophthalmus) is an important freshwater teleost that is now widely farmed across the Mekong River Delta in Vietnam. Understanding the basis for tolerance and adaptation to raised environmental salinity conditions can assist the regional culture industry to mitigate predicted impacts of climate change across this region. Attempt of next generation sequencing using the ion proton platform results in more than 174 million raw reads from three tissue libraries (gill, kidney and intestine). Reads were filtered and de novo assembled using a variety of assemblers and then clustered together to generate a combined reference transcriptome. Downstream analysis resulted in a final reference transcriptome that contained 60,585 transcripts with an N50 of 683 bp. This resource was further annotated using a variety of bioinformatics databases, followed by differential gene expression analysis that resulted in 3062 transcripts that were differentially expressed in catfish samples raised under two experimental conditions (0 and 15 ppt). A number of transcripts with a potential role in salinity tolerance were then classified into six different functional gene categories based on their gene ontology assignments. These included; energy metabolism, ion transportation, detoxification, signal transduction, structural organization and detoxification. Finally, we combined the data on functional salinity tolerance genes into a hypothetical schematic model that attempted to describe potential relationships and interactions among target genes to explain the molecular pathways that control adaptive salinity responses in P. hypophthalmus. Our results indicate that P. hypophthalmus exhibit predictable plastic regulatory responses to elevated salinity by means of characteristic gene expression patterns, providing numerous candidate genes for future investigations.

The study of genetic diversity and population structure of the Korean fleshy shrimp, Fenneropenaeus chinensis, using newly developed microsatellite markers

The fleshy shrimp, Fenneropenaeus chinensis, is the family of Penaeidae and one of the most economically important marine culture species in Korea. However, its genetic characteristics have never been studied. In this study, a total of 240 wild F. chinensis individuals were collected from four locations as follows: Narodo (NRD, n = 60), Beopseongpo (BSP, n = 60), Chaesukpo (CSP, n = 60), and Cheonsuman (CSM, n = 60). Genetic variability and the relationships among four wild F. chinensis populations were analyzed using 13 newly developed microsatellite loci. Relatively high levels of genetic variability (mean allelic richness = 16.87; mean heterozygosity = 0.845) were found among localities. Among the 52 population loci, 13 showed significant deviation from the Hardy–Weinberg equilibrium. Neighbor-joining, principal coordinate, and molecular variance analyses revealed the presence of three subpopulations (NRD, CSM, BSP and CSP), which was consistent with clustering based on genetic distance. The mean observed heterozygosity values of the NRD, CSM, BSP, and CSP populations were 0.724, 0.821, 0.814, and 0.785 over all loci, respectively. These genetic variability and differentiation results of the four wild populations can be applied for future genetic improvement using selective breeding and to design suitable management guidelines for Korean F. chinensis culture.

Fate of key food-borne pathogens associated with intensive pig and poultry farming environments

Intensive pig and poultry farming in Australia can be a source of pathogens with implications for food-safety and/or human illness. Seven studies were undertaken with the following objectives: · Assess the types of zoonotic pathogens in waste · Assess the transfer of pathogens during re-use both within the shed and externally in the environment · The potential for movement of pathogens via aerosols In the first and second studies the extent of zoonotic pathogens was evaluated in both piggery effluent and chicken litter and Salmonella and Campylobacter were detected in both wastes. In the third study the dynamics of Salmonella during litter re-use was examined and results showed a trend for lower Salmonella levels and serovar diversity in re-used litter compared to new litter. Thus, re-use within the poultry farming system posed no increased risk. The fourth study addressed the direct risks of pathogens to farm workers due to reuse of piggery effluent within the pig shed. Based on air-borne Escherichia coli (E. coli) levels, re-using effluent did not pose a risk. In the fifth study high levels of Arcobacter spp. were detected in effluent ponds and freshly irrigated soils with potential food-safety risks during the irrigation of food-crops and pasture. The sixth and seventh studies addressed the risks from aerosols from mechanically ventilated sheds. Staphylococci were shown to have potential as markers, with airborne levels gradually dropping and reaching background levels at 400 m distance. Salmonella was detected (at low levels) both inside and outside the shed (at 10 m). Campylobacter was detected only once inside the shed during the 3-year period (at low levels). Results showed there was minimal risk to humans living adjacent to poultry farms This is the first comprehensive analysis studying key food-safety pathogens and potential public health risks associated with intensively farmed pigs and poultry in Australia.

Natural host range, thrips and seed transmission of distinct Tobacco streak virus strains in Queensland, Australia

Diseases caused by Tobacco streak virus (TSV) have resulted in significant crop losses in sunflower and mung bean crops in Australia. Two genetically distinct strains from central Queensland, TSV-parthenium and TSV-crownbeard, have been previously described. They share only 81% total-genome nucleotide sequence identity and have distinct major alternative hosts, Parthenium hysterophorus (parthenium) and Verbesina encelioides (crownbeard). We developed and used strain-specific multiplex Polymerase chain reactions (PCRs) for the three RNA segments of TSV-parthenium and TSV-crownbeard to accurately characterise the strains naturally infecting 41 hosts species. Hosts included species from 11 plant families, including 12 species endemic to Australia. Results from field surveys and inoculation tests indicate that parthenium is a poor host of TSV-crownbeard. By contrast, crownbeard was both a natural host of, and experimentally infected by TSV-parthenium but this infection combination resulted in non-viable seed. These differences appear to be an effective biological barrier that largely restricts these two TSV strains to their respective major alternative hosts. TSV-crownbeard was seed transmitted from naturally infected crownbeard at a rate of between 5% and 50% and was closely associated with the geographical distribution of crownbeard in central Queensland. TSV-parthenium and TSV-crownbeard were also seed transmitted in experimentally infected ageratum (Ageratum houstonianum) at rates of up to 40% and 27%, respectively. The related subgroup 1 ilarvirus, Ageratum latent virus, was also seed transmitted at a rate of 18% in ageratum which is its major alternative host. Thrips species Frankliniella schultzei and Microcephalothrips abdominalis were commonly found in flowers of TSV-affected crops and nearby weed hosts. Both species readily transmitted TSV-parthenium and TSV-crownbeard. The results are discussed in terms of how two genetically and biologically distinct TSV strains have similar life cycle strategies in the same environment.

Consumption of crops by feral pigs (Sus scrofa) in a fragmented agricultural landscape

Feral pigs (Sus scrofa) consume and damage crops and impact the environment through predation, competition and habitat disturbance, although supporting dietary data are lacking in agricultural landscapes. This study was undertaken to determine the relative importance of food items in the diet of feral pigs in a fragmented agricultural landscape, particularly to assist in predicting the breadth of likely impacts. Diet composition was assessed from the stomach contents of 196 feral pigs from agricultural properties in southern Queensland. Feral pigs were herbivorous, with plant matter comprising >99% of biomass consumed. Crops were consumed more frequently than non-crop species, and comprised >60% of dietary biomass, indicating a clear potential for direct economic losses. Consumption of pasture and forage species also suggests potential competition for pasture with domestic stock. There is little evidence of direct predation on native fauna, but feral pig feeding activities may impact environmental values. Seasonal differences in consumption of crop, pasture or animal food groups probably reflect the changing availability of food items. We recommend that future dietary studies examine food availability to determine any dietary preferences to assist in determining the foods most susceptible to damage. The outcomes of this study are important for developing techniques for monitoring the impacts of feral pigs, essential for developing management options to reduce feral pig damage on agricultural lands.

Stable expression of silencing-suppressor protein enhances the performance and longevity of an engineered metabolic pathway

Transgenic engineering of plants is important in both basic and applied research. However, the expression of a transgene can dwindle over time as the plant's small (s)RNA-guided silencing pathways shut it down. The silencing pathways have evolved as antiviral defence mechanisms, and viruses have co-evolved viral silencing-suppressor proteins (VSPs) to block them. Therefore, VSPs have been routinely used alongside desired transgene constructs to enhance their expression in transient assays. However, constitutive, stable expression of a VSP in a plant usually causes pronounced developmental abnormalities, as their actions interfere with endogenous microRNA-regulated processes, and has largely precluded the use of VSPs as an aid to stable transgene expression. In an attempt to avoid the deleterious effects but obtain the enhancing effect, a number of different VSPs were expressed exclusively in the seeds of Arabidopsis thaliana alongside a three-step transgenic pathway for the synthesis of arachidonic acid (AA), an ω-6 long chain polyunsaturated fatty acid. Results from independent transgenic events, maintained for four generations, showed that the VSP-AA-transformed plants were developmentally normal, apart from minor phenotypes at the cotyledon stage, and could produce 40% more AA than plants transformed with the AA transgene cassette alone. Intriguingly, a geminivirus VSP, V2, was constitutively expressed without causing developmental defects, as it acts on the siRNA amplification step that is not part of the miRNA pathway, and gave strong transgene enhancement. These results demonstrate that VSP expression can be used to protect and enhance stable transgene performance and has significant biotechnological application.

Spatial and temporal determinants of Finnish farmland bird populations

During the past decades agricultural intensification has caused dramatic population declines in a wide range of taxa related to farmland habitats, including farmland birds. In this thesis, I studied how boreal farmland landscape characteristics and agricultural land use affect the abundance and diversity of farmland birds using extensive field data collected by territory mapping of breeding farmland birds in various parts of Finland. My results show that the area and openness of agricultural areas are key determinants of farmland bird abundance and distribution. A landscape composition with enough open farmland combined with key habitats such as farmyards and wetland is likely to provide essential prerequisites for the occurrence of a rich farmland avifauna. In Finland, the majority of large areas suitable for open habitat specialists are located in southern and western parts of the country. However, the diversity of the species with an unfavourable conservation status in Europe (SPECs) had notable hotspot areas in northern and north-western agricultural areas. I found that in boreal agroecosystems farmland birds favour fields with springtime vegetative cover, especially agricultural grasslands and set-asides. Hence, in the spring cereal dominated Finnish agroecosystems it is the absence of field vegetation that may limit populations of many farmland bird species. It is likely that the decrease of crops providing vegetative cover in the spring, such as permanent grasslands, cultivated grass, and autumn-sown cereals, has greatly contributed to the declines of Finnish farmland birds. Grass crops have persistently declined in Finland as a consequence of specialization in crop production and the large-scale decline in livestock husbandry. Small-scale non-crop habitats, especially ditches and ditch margins, are also important for many bird species in the Finnish agroecosystems, but have dramatically declined during the last decades. A major problem for farmland bird conservation in Finland is the conflict between landscape structure and agricultural management. Areas with mixed and cattle farming are virtually absent from the large agricultural plains of southern and south-western Finland, where the landscape structure is more likely to be favourable for rich farmland bird assemblages. On the other hand, mixed and cattle farming is still rather frequent in northern and central parts of the country, where the landscape structure is not suitable for many farmland specialist birds requiring open landscapes. My results provide useful guidelines for farmland bird conservation, and imply that considerable attention needs to be paid to landscape factors when selecting areas for various conservational management actions, such as agri-environment schemes. Actions promoting the abundance of set-asides, grass crops, and ditches would markedly benefit Finnish farmland bird populations. Organic farming may benefit farmland birds, but it is not clear how general its beneficial effect is in boreal agroecosystems. The most urgent action aiming to preserve farmland biodiversity would be to support re-introducing and sustaining cattle farming by environmental subsidies. This would be especially beneficial in the southern parts of Finland, where the landscape characteristics and abundance of agricultural areas are most suitable for farmland birds and where cattle farming is currently rare.

Effects of glycerol on enzymatic hydrolysis and ethanol production using sugarcane bagasse pretreated by acidified glycerol solution

In this study, for the first time the effects of glycerol on enzymatic hydrolysis and ethanol fermentation were investigated. Enzymatic hydrolysis was inhibited slightly with 2.0 wt% glycerol, leading to reduction in glucan digestibility from 84.9% without glycerol to 82.9% (72 h). With 5.0 wt% and 10.0 wt% glycerol, glucan digestibility reduced by 4.5% and11.0%, respectively. However, glycerol appeared not detrimental to cellulase enzymes. Ethanol fermentation was not affected with glycerol up to 5.0 wt%, and was inhibited slightly with 10.0 wt% glycerol, which resulted in reduction in ethanol yield from 86.0% without glycerol to 83.7% (20 h). Based on laboratory and pilot scale enzymatic hydrolysis and ethanol production results, it was estimated that 0.142 kg ethanol could be produced from 1.0 kg dry bagasse (a glucan content of 38.0%) after pretreatment with acidified glycerol solution.

Microbial oil production from sugarcane bagasse hydrolysates by oleaginous yeast and filamentous fungi

This study investigated the potential use of sugarcane bagasse as a feedstock for oil production through microbial cultivation. Bagasse was subjected to dilute acid pretreatment with 0.4 wt% H2SO4 (in liquid) at a solid/liquid ratio of 1:6 (wt/wt) at 170 °C for 15 min, followed by enzymatic hydrolysis of solid residue. The liquid fractions of the pretreatment process and the enzymatic hydrolysis process were detoxified and used as liquid hydrolysate (SCBLH) and enzymatic hydrolysate (SCBEH) for the microbial oil production by oleaginous yeast (Rhodotorula mucilaginosa) and filamentous fungi (Aspergillus oryzae and Mucor plumbeus). The results showed that all strains were able to grow and produce oil from bagasse hydrolysates. The highest oil concentrations produced from bagasse hydrolysates were by M. plumbeus at 1.59 g/L (SCBLH) and 4.74 g/L (SCBEH). The microbial oils obtained have similar fatty acid compositions to vegetable oils, indicating that the oil can be used for the production of second generation biodiesel. On the basis of oil yields obtained by M. plumbeus, from 10 million t (wet weight) of bagasse generated annually from sugar mills in Australia, it is estimated that the total biodiesel that could be produced would be equivalent to about 9% of Queensland’s diesel consumption.

Trehalose accumulation triggers autophagy during plant desiccation

Global climate change, increasingly erratic weather and a burgeoning global population are significant threats to the sustainability of future crop production. There is an urgent need for the development of robust measures that enable crops to withstand the uncertainty of climate change whilst still producing maximum yields. Resurrection plants possess the unique ability to withstand desiccation for prolonged periods, can be restored upon watering and represent great potential for the development of stress tolerant crops. Here, we describe the remarkable stress characteristics of Tripogon loliiformis, an uncharacterised resurrection grass and close relative of the economically important cereals, rice, sorghum, and maize. We show that T. loliiformis survives extreme environmental stress by implementing autophagy to prevent Programmed Cell Death. Notably, we identified a novel role for trehalose in the regulation of autophagy in T.loliiformis. Transcriptome, Gas Chromatography Mass Spectrometry, immunoblotting and confocal microscopy analyses directly linked the accumulation of trehalose with the onset of autophagy in dehydrating and desiccated T. loliiformis shoots. These results were supported in vitro with the observation of autophagosomes in trehalose treated T. loliiformis leaves; autophagosomes were not detected in untreated samples. Presumably, once induced, autophagy promotes desiccation tolerance in T.loliiformis , by removal of cellular toxins to suppress programmed cell death and the recycling of nutrients to delay the onset of senescence. These findings illustrate how resurrection plants manipulate sugar metabolism to promote desiccation tolerance and may provide candidate genes that are potentially useful for the development of stress tolerant crops.

Tripogon loliiformis elicits a rapid physiological and structural response to dehydration for desiccation tolerance

Resurrection plants can withstand extreme dehydration to an air-dry state and then recover upon receiving water. Tripogon loliiformis (F.Muell.) C.E.Hubb. is a largely uncharacterised native Australian desiccation-tolerant grass that resurrects from the desiccated state within 72 h. Using a combination of structural and physiological techniques the structural and physiological features that enable T. loliiformis to tolerate desiccation were investigated. These features include: - (i) a myriad of structural changes such as leaf folding, cell wall folding and vacuole fragmentation that mitigate desiccation stress; - (ii) potential role of sclerenchymatous tissue within leaf folding and radiation protection; - (iii) retention of ~70% chlorophyll in the desiccated state; - (iv) early response of photosynthesis to dehydration by 50% reduction and ceasing completely at 80 and 70% relative water content, respectively; - (v) a sharp increase in electrolyte leakage during dehydration, and; - (vi) confirmation of membrane integrity throughout desiccation and rehydration. Taken together, these results demonstrate that T. loliiformis implements a range of structural and physiological mechanisms that minimise mechanical, oxidative and irradiation stress. These results provide powerful insights into tolerance mechanisms for potential utilisation in the enhancement of stress-tolerance in crop plants.

The influence of impurities on calcium phosphate floc structure and size in sugar solutions

Settling, dewatering and filtration of flocs are important steps in industry to remove solids and improve subsequent processing. The influence of non-sucrose impurities (Ca2+, Mg2+, phosphate and aconitic acid) on calcium phosphate floc structure (scattering exponent, Sf), size and shape were examined in synthetic and authentic sugar juices using X-ray diffraction techniques. In synthetic juices, Sf decreases with increasing phosphate concentration to values where loosely bound and branched flocs are formed for effective trapping and removal of impurities. Although, Sf did not change with increasing aconitic acid concentration, the floc size significantly decreased reducing the ability of the flocs to remove impurities. In authentic juices, the flocs structures were marginally affected by increasing proportions of non-sucrose impurities. However, optical microscopy indicated the formation of well-formed macro-floc network structures in sugar cane juices containing lower proportions of non-sucrose impurities. These structures are better placed to remove suspended colloidal solids.

Pulp and paper production from sugarcane bagasse

The pulp and paper industry is very large and is now well in excess of $200 billion (FAO 2009). Estimates for the amount of bagasse used in the production of pulp and paper products vary but the general consensus is that it accounts for 2–5% of global production, making it one of the highest revenue earners for the global sugarcane industry.

Complete genome sequence of a novel zantedeschia mild mosaic virus isolate: The first report from Australia and from Alocasia sp

The complete genome of an Australian isolate of zantedeschia mild mosaic virus (ZaMMV) causing mosaic symptoms on Alocasia sp. (designated ZaMMVAU) was cloned and sequenced. The genome comprises 9942 nucleotides (excluding the poly-A tail) and encodes a polyprotein of 3167 amino acids. The sequence is most closely related to a previously reported ZaMMV isolate from Taiwan (ZaMMV-TW), with 82 and 86 % identity at the nucleotide and amino acid level, respectively. Unlike the amino acid sequence of ZaMMV-TW, however, ZaMMV-AU does not contain a polyglutamine stretch at the N-terminus of the coat-protein-coding region upstream of the DAG motif. This is the first report of ZaMMV from Australia and from Alocasia sp.