Aboveground plant biomass from the Jena Experiment (Monocultures, year 2007)

This data set contains aboveground plant biomass in 2007 (Sown plant community, Weed plant community, Dead plant material, and Unidentified plant material; all measured in biomass as dry weight) of the monoculture plots of a large grassland biodiversity experiment (the Jena Experiment). In the monoculture plots the biomass of the sown plant community contains only a single species per plot and this species is a different one for each plot. Which species has been sown in which plot is stated in the plot information table for monocultures (see further details below). The monoculture plots of 3.5 x 3.5 m were established for all of the 60 plant species of the Jena Experiment species pool with two replicates per species. These 60 species comprising the species pool of the Jena Experiment belong to four functional groups (grasses, legumes, tall and small herbs). Plots were sown in May 2002 and are since maintained by bi-annual weeding and mowing. Aboveground plant biomass was harvested twice in 2007 just prior to mowing (during peak standing biomass in early June and in late August) on all experimental plots of the monocultures. This was done by clipping the vegetation at 3 cm above ground in 2 rectangles of 0.2 x 0.5 m per plot. The location of these rectangles was assigned prior to each harvest by random selection of coordinates within the core area of the plots (i.e. excluding an outer edge of 0.5 m). The positions of the rectangles within plots were identical for all plots. The harvested biomass was sorted into categories: sown plant species, weed plant species (species not sown at the particular plot), detached dead plant material (i.e., dead plant material in the data file), and remaining plant material that could not be assigned to any category (i.e., unidentified plant material in the data file). All biomass was dried to constant weight (70°C, >= 48 h) and weighed. The data for individual subsamples (i.e. rectangles) and the mean over samples for all biomass measures are given.

Aboveground plant community and species-specific vegetation cover from the Jena Experiment (Main Experiment, year 2007)

This data set contains information on vegetation cover, i.e. the proportion of soil surface area that is covered by different categories of plants per estimated plot area. Data was collected on the plant community level (sown plant community, weed plant community, dead plant material, and bare ground) and on the level of individual plant species in case of the sown species. Data presented here is from the Main Experiment plots of a large grassland biodiversity experiment (the Jena Experiment; see further details below). In the main experiment, 82 grassland plots of 20 x 20 m were established from a pool of 60 species belonging to four functional groups (grasses, legumes, tall and small herbs). In May 2002, varying numbers of plant species from this species pool were sown into the plots to create a gradient of plant species richness (1, 2, 4, 8, 16 and 60 species) and functional richness (1, 2, 3, 4 functional groups). Plots were maintained by bi-annual weeding and mowing. In 2007, vegetation cover was estimated twice in June and August just prior to mowing (during peak standing biomass) on all experimental plots of the Main Experiment. Cover was visually estimated in a central area of each plot 3 by 3 m in size (approximately 9 m²) using a decimal scale (Londo). Cover estimates for the individual species (and for target species + weeds + bare ground) can add up to more than 100% because the estimated categories represented a structure with potentially overlapping multiple layers. In 2007, dead plant material was found only in a few plots. Therefore, cover of dead plant material is zero for most of the 82 plots.

Aboveground plant community and species-specific vegetation cover from the Jena Experiment (Main Experiment, year 2004)

This data set contains information on vegetation cover, i.e. the proportion of soil surface area that is covered by different categories of plants per estimated plot area. Data was collected on the plant community level (sown plant community, weed plant community, dead plant material, and bare ground) and on the level of individual plant species in case of the sown species. Data presented here is from the Main Experiment plots of a large grassland biodiversity experiment (the Jena Experiment; see further details below). In the main experiment, 82 grassland plots of 20 x 20 m were established from a pool of 60 species belonging to four functional groups (grasses, legumes, tall and small herbs). In May 2002, varying numbers of plant species from this species pool were sown into the plots to create a gradient of plant species richness (1, 2, 4, 8, 16 and 60 species) and functional richness (1, 2, 3, 4 functional groups). Plots were maintained by bi-annual weeding and mowing. In 2004, vegetation cover was estimated twice in May and August just prior to mowing (during peak standing biomass) on all experimental plots of the Main Experiment. Cover was visually estimated in a central area of each plot 3 by 3 m in size (approximately 9 m²) using a decimal scale (Londo). Cover estimates for the individual species (and for target species + weeds + bare ground) can add up to more than 100% because the estimated categories represented a structure with potentially overlapping multiple layers. In 2004, cover on the community level was only estimated for the sown plant community, weed plant community and bare soil. In contrast to later years, cover of dead plant material was not estimated.

Aboveground plant biomass from the Jena Experiment (Monocultures, year 2008)

This data set contains aboveground plant biomass in 2008 (Sown plant community, Weed plant community, Dead plant material, and Unidentified plant material; all measured in biomass as dry weight) of the monoculture plots of a large grassland biodiversity experiment (the Jena Experiment). In the monoculture plots the biomass of the sown plant community contains only a single species per plot and this species is a different one for each plot. Which species has been sown in which plot is stated in the plot information table for monocultures (see further details below). The monoculture plots of 3.5 x 3.5 m were established for all of the 60 plant species of the Jena Experiment species pool with two replicates per species. One of the replicate plots per species was given up after the vegetation period of 2007 for all but the nine species belonging also to the so called dominance experiment in Jena. These nine species are: Alopecurus pratensis, Anthriscus sylvestris, Arrhenatherum elatius, Dactylis glomerata, Geranium pratense, Poa trivialis, Phleum pratense, Trifolium repens and Trifolium pratense.In 2008 plot size was reduced to 2.5 x 2.5 m. These 60 species comprising the species pool of the Jena Experiment belong to four functional groups (grasses, legumes, tall and small herbs). Plots were sown in May 2002 and are since maintained by bi-annual weeding and mowing. Aboveground plant biomass was harvested twice in 2008 just prior to mowing (during peak standing biomass in early June and in late August) on all experimental plots of the monocultures. This was done by clipping the vegetation at 3 cm above ground in 2 rectangles of 0.2 x 0.5 m per plot. The location of these rectangles was assigned prior to each harvest by random selection of coordinates within the core area of the plots (i.e. excluding an outer edge of 0.5 m). The positions of the rectangles within plots were identical for all plots. The harvested biomass was sorted into categories: sown plant species, weed plant species (species not sown at the particular plot), detached dead plant material (i.e., dead plant material in the data file), and remaining plant material that could not be assigned to any category (i.e., unidentified plant material in the data file). All biomass was dried to constant weight (70°C, >= 48 h) and weighed. The data for individual subsamples (i.e. rectangles) and the mean over samples for all biomass measures are given.

Aboveground plant biomass from the Jena Experiment (Monocultures, year 2009)

This data set contains aboveground plant biomass in 2009 (Sown plant community, Weed plant community, Dead plant material, and Unidentified plant material; all measured in biomass as dry weight) of the monoculture plots of a large grassland biodiversity experiment (the Jena Experiment). In the monoculture plots the biomass of the sown plant community contains only a single species per plot and this species is a different one for each plot. Which species has been sown in which plot is stated in the plot information table for monocultures (see further details below). The monoculture plots of 3.5 x 3.5 m were established for all of the 60 plant species of the Jena Experiment species pool with two replicates per species. One of the replicate plots per species was given up after the vegetation period of 2007 for all but the nine species belonging also to the so called dominance experiment in Jena. These nine species are: Alopecurus pratensis, Anthriscus sylvestris, Arrhenatherum elatius, Dactylis glomerata, Geranium pratense, Poa trivialis, Phleum pratense, Trifolium repens and Trifolium pratense.In 2008 plot size was reduced to 2.5 x 2.5 m. These 60 species comprising the species pool of the Jena Experiment belong to four functional groups (grasses, legumes, tall and small herbs). Plots were sown in May 2002 and are since maintained by bi-annual weeding and mowing. Aboveground plant biomass was harvested twice in 2009 just prior to mowing (during peak standing biomass in early June and in late August) on all experimental plots of the monocultures. This was done by clipping the vegetation at 3 cm above ground in 2 rectangles of 0.2 x 0.5 m per plot. The location of these rectangles was in the center of the plot area. The positions of the rectangles within plots were identical for all plots. The harvested biomass was sorted into categories: sown plant species, weed plant species (species not sown at the particular plot), detached dead plant material (i.e., dead plant material in the data file), and remaining plant material that could not be assigned to any category (i.e., unidentified plant material in the data file). All biomass was dried to constant weight (70°C, >= 48 h) and weighed. The data for individual subsamples (i.e. rectangles) and the mean over samples for all biomass measures are given.

Aboveground plant biomass from the Jena Experiment (Monocultures, year 2004)

This data set contains aboveground plant biomass in 2004 (Sown plant community, Weed plant community, Dead plant material, and Unidentified plant material; all measured in biomass as dry weight) of the monoculture plots of a large grassland biodiversity experiment (the Jena Experiment). In the monoculture plots the biomass of the sown plant community contains only a single species per plot and this species is a different one for each plot. Which species has been sown in which plot is stated in the plot information table for monocultures (see further details below). The monoculture plots of 3.5 x 3.5 m were established for all of the 60 plant species of the Jena Experiment species pool with two replicates per species. These 60 species comprising the species pool of the Jena Experiment belong to four functional groups (grasses, legumes, tall and small herbs). Plots were sown in May 2002 and are since maintained by bi-annual weeding and mowing. Aboveground plant biomass was harvested twice in 2004 just prior to mowing (during peak standing biomass in early June and in late August) on all experimental plots of the monocultures. This was done by clipping the vegetation at 3 cm above ground in 2 rectangles of 0.2 x 0.5 m per plot. The location of these rectangles was assigned prior to each harvest by random selection of coordinates within the core area of the plots (i.e. excluding an outer edge of 0.5 m). The positions of the rectangles within plots were identical for all plots. The harvested biomass was sorted into categories: sown plant species, weed plant species (species not sown at the particular plot), detached dead plant material (i.e., dead plant material in the data file), and remaining plant material that could not be assigned to any category (i.e., unidentified plant material in the data file). All biomass was dried to constant weight (70°C, >= 48 h) and weighed. The data for individual subsamples (i.e. rectangles) and the mean over samples for all biomass measures are given.

Exploring plant tissue culture to improve the production of phenolic compounds: A review

Plant tissue and organ culture has been extensively used from the beginning of the XX century for the study and comprehension of some primary biological mechanisms such as morphogenesis. However, with the increasing demand of the market for novel products derived from plants, in vitro culture became a reliable technique for the mass production of plant material. Moreover, the potential to use this technique for the production of some bioactive compounds, such as phenolic compounds, is immense since it allows the manipulation of the biosynthetic routes to increase the production and accumulation of specific compounds. This work intends to make a brief historical review of in vitro culture, highlighting its use for the production of bioactive compounds. Also, emphasizes the importance of phenolic compounds for the consumer as well reviews the metabolic pathways involved in its production in plant cells. Furthermore, it was carried out a comprehensive study on the work developed for the production of plant phenolic compounds in in vitro cultures, as well as on the type of elicitors used to increase of the same production; also a brief highlighting of the phenolic compounds which serve as elicitors. There are numerous reports directed to the production of phenolic extracts in in vitro plant cultures, however there is a lack in the production of individual phenolic compounds mainly due to the complexity of the biosynthetic routes and extraction procedures. Elicitation procedures are often used to increase the production of phenolics, archieving in most cases higher yields than in non-elicitated cultures. The increasing production of bioactive phenolic extracts/compounds allows for their further applicability, namely in the industry of functional foods or in pharmaceutical/medical fields.

Optimisation of Banana streak virus (BSV) diagnostic assays

Bananas are one of the world�fs most important crops, serving as a staple food and an important source of income for millions of people in the subtropics. Pests and diseases are a major constraint to banana production. To prevent the spread of pests and disease, farmers are encouraged to use disease�] and insect�]free planting material obtained by micropropagation. This option, however, does not always exclude viruses and concern remains on the quality of planting material. Therefore, there is a demand for effective and reliable virus indexing procedures for tissue culture (TC) material. Reliable diagnostic tests are currently available for all of the economically important viruses of bananas with the exception of Banana streak viruses (BSV, Caulimoviridae, Badnavirus). Development of a reliable diagnostic test for BSV is complicated by the significant serological and genetic variation reported for BSV isolates, and the presence of endogenous BSV (eBSV). Current PCR�] and serological�]based diagnostic methods for BSV may not detect all species of BSV, and PCR�]based methods may give false positives because of the presence of eBSV. Rolling circle amplification (RCA) has been reported as a technique to detect BSV which can also discriminate between episomal and endogenous BSV sequences. However, the method is too expensive for large scale screening of samples in developing countries, and little information is available regarding its sensitivity. Therefore the development of reliable PCR�]based assays is still considered the most appropriate option for large scale screening of banana plants for BSV. This MSc project aimed to refine and optimise the protocols for BSV detection, with a particular focus on developing reliable PCR�]based diagnostics Initially, the appropriateness and reliability of PCR and RCA as diagnostic tests for BSV detection were assessed by testing 45 field samples of banana collected from nine districts in the Eastern region of Uganda in February 2010. This research was also aimed at investigating the diversity of BSV in eastern Uganda, identifying the BSV species present and characterising any new BSV species. Out of the 45 samples tested, 38 and 40 samples were considered positive by PCR and RCA, respectively. Six different species of BSV, namely Banana streak IM virus (BSIMV), Banana streak MY virus (BSMYV), Banana streak OL virus (BSOLV), Banana streak UA virus (BSUAV), Banana streak UL virus (BSULV), Banana streak UM virus (BSUMV), were detected by PCR and confirmed by RCA and sequencing. No new species were detected, but this was the first report of BSMYV in Uganda. Although RCA was demonstrated to be suitable for broad�]range detection of BSV, it proved time�]consuming and laborious for identification in field samples. Due to the disadvantages associated with RCA, attempts were made to develop a reliable PCR�]based assay for the specific detection of episomal BSOLV, Banana streak GF virus (BSGFV), BSMYV and BSIMV. For BSOLV and BSGFV, the integrated sequences exist in rearranged, repeated and partially inverted portions at their site of integration. Therefore, for these two viruses, primers sets were designed by mapping previously published sequences of their endogenous counterparts onto published sequences of the episomal genomes. For BSOLV, two primer sets were designed while, for BSGFV, a single primer set was designed. The episomalspecificity of these primer sets was assessed by testing 106 plant samples collected during surveys in Kenya and Uganda, and 33 leaf samples from a wide range of banana cultivars maintained in TC at the Maroochy Research Station of the Department of Employment, Economic Development and Innovation (DEEDI), Queensland. All of these samples had previously been tested for episomal BSV by RCA and for both BSOLV and BSGFV by PCR using published primer sets. The outcome from these analyses was that the newly designed primer sets for BSOLV and BSGFV were able to distinguish between episomal BSV and eBSV in most cultivars with some B�]genome component. In some samples, however, amplification was observed using the putative episomal�]specific primer sets where episomal BSV was not identified using RCA. This may reflect a difference in the sensitivity of PCR compared to RCA, or possibly the presence of an eBSV sequence of different conformation. Since the sequences of the respective eBSV for BSMYV and BSIMV in the M. balbisiana genome are not available, a series of random primer combinations were tested in an attempt to find potential episomal�]specific primer sets for BSMYV and BSIMV. Of an initial 20 primer combinations screened for BSMYV detection on a small number of control samples, 11 primers sets appeared to be episomal�]specific. However, subsequent testing of two of these primer combinations on a larger number of control samples resulted in some inconsistent results which will require further investigation. Testing of the 25 primer combinations for episomal�]specific detection of BSIMV on a number of control samples showed that none were able to discriminate between episomal and endogenous BSIMV. The final component of this research project was the development of an infectious clone of a BSV endemic in Australia, namely BSMYV. This was considered important to enable the generation of large amounts of diseased plant material needed for further research. A terminally redundant fragment (.1.3 �~ BSMYV genome) was cloned and transformed into Agrobacterium tumefaciens strain AGL1, and used to inoculate 12 healthy banana plants of the cultivars Cavendish (Williams) by three different methods. At 12 weeks post�]inoculation, (i) four of the five banana plants inoculated by corm injection showed characteristic BSV symptoms while the remaining plant was wilting/dying, (ii) three of the five banana plants inoculated by needle�]pricking of the stem showed BSV symptoms, one plant was symptomless while the remaining had died and (iii) both banana plants inoculated by leaf infiltration were symptomless. When banana leaf samples were tested for BSMYV by PCR and RCA, BSMYV was confirmed in all banana plants showing symptoms including those were wilting and/or dying. The results from this research have provided several avenues for further research. By completely sequencing all variants of eBSOLV and eBSGFV and fully sequencing the eBSIMV and eBSMYV regions, episomal BSV�]specific primer sets for all eBSVs could potentially be designed that could avoid all integrants of that particular BSV species. Furthermore, the development of an infectious BSV clone will enable large numbers of BSVinfected plants to be generated for the further testing of the sensitivity of RCA compared to other more established assays such as PCR. The development of infectious clones also opens the possibility for virus induced gene silencing studies in banana.

Identification of a putative cellulase gene in the giant freshwater prawn, Macrobrachium rosenbergii (De Man, 1879)

Nutrition plays an important role in the development of all organisms and in particular that of farmed aquatic species where costs associated with feed can often exceed 60% of total production costs. Crustacean species in addition, have the added metabolic requirement for regular moulting to allow normal growth and this requires large amounts of energy in the form of sugars (glucose). The current study explored the capacity of the giant freshwater prawn to produce endogenous cellulose-degrading enzymes capable of extracting nutrients (simple sugars) from plant sources in formulated feeds used in the prawn aquaculture industry. We identified a putative cellulase cDNA fragment in the target organism of 1576 base pairs in length of non-microbial origin that after protein modelling exhibited a TM-score of 0.916 with a described cellulase reported from another crustacean species. The functional role of cellulase enzymes is to hydrolyse cellulose to glucose and the fragment identified in GFP was highly expressed in the hepatopancreas, the site of primary food digestion and absorption in crustaceans. Hepatopancreatic tissue from Macrobrachium rosenbergii also showed active digestion of cellulose to glucose following an endoglucanase assay. Cellulase gene(s) are present in the genomes of many invertebrate taxa and play an active role in the conversion of cellulose to available energy. Identification and characterization of endogenous cellulase gene(s) in giant freshwater prawn can assist development of the culture industry because the findings confirm that potentially greater levels of low-cost plant-material could be included in artificial formulated diets in the future without necessarily compromising individual growth performance. Ultimately, this development may contribute to more efficient, cost-effective production systems for freshwater prawn culture stocks that meet the animal's basic nutritional requirements and that also support good individual growth rates.

Fate of applied biosolids nitrogen in a cut and remove forage system on an alluvial clay loam soil

The fate of nitrogen (N) applied in biosolids was investigated in a forage production system on an alluvial clay loam soil in south-eastern Queensland, Australia. Biosolids were applied in October 2002 at rates of 6, 12, 36, and 54dryt/ha for aerobically digested biosolids (AE) and 8, 16, 48, and 72dryt/ha for anaerobically digested biosolids (AN). Rates were based on multiples of the Nitrogen Limited Biosolids Application rate (0.5, 1, 3, and 4.5NLBAR) for each type of biosolid. The experiment included an unfertilised control and a fertilised control that received multiple applications of synthetic fertiliser. Forage sorghum was planted 1 week after biosolids application and harvested 4 times between December 2002 and May 2003. Dry matter production was significantly greater from the biosolids-treated plots (21-27t/ha) than from the unfertilised (16t/ha) and fertilised (18t/ha) controls. The harvested plant material removed an extra 148-488kg N from the biosolids-treated plots. Partial N budgets were calculated for the 1NLBAR and 4.5NLBAR treatments for each biosolids type at the end of the crop season. Crop removal only accounted for 25-33% of the applied N in the 1NLBAR treatments and as low as 8-15% with 4.5NLBAR. Residual biosolids N was predominantly in the form of organic N (38-51% of applied biosolids N), although there was also a significant proportion (10-23%) as NO3-N, predominantly in the top 0.90m of the soil profile. From 12 to 29% of applied N was unaccounted for, and presumed to be lost as gaseous nitrogen and/or ammonia, as a consequence of volatilisation or denitrification, respectively. In-season mineralisation of organic N in biosolids was 43-59% of the applied organic N, which was much greater than the 15% (AN)-25% (AE) expected, based on current NLBAR calculation methods. Excessive biosolids application produced little additional biomass but led to high soil mineral N concentrations that were vulnerable to multiple loss pathways. Queensland Guidelines need to account for higher rates of mineralisation and losses via denitrification and volatilisation and should therefore encourage lower application rates to achieve optimal plant growth and minimise the potential for detrimental impacts on the environment.

Analysis of Daphnane Orthoesters in Poisonous Australian Pimelea Species by Liquid Chromatography-Tandem Mass Spectrometry.

Cattle grazing in arid rangelands of Australia suffer periodic extensive and serious poisoning by the plant species Pimelea trichostachya, P. simplex, and P. elongata. Pimelea poisoning (also known as St. George disease and Marree disease) has been attributed to the presence of the diterpenoid orthoester simplexin in these species. However, literature relating to previous studies is complicated by taxonomic revisions, and the presence of simplexin has not previously been verified in all currently recognized taxa capable of inducing pimelea poisoning syndrome, with no previous chemical studies of P. trichostachya (as currently classified) or P. simplex subsp. continua. We report here the isolation of simplexin from P. trichostachya and the development of a liquid chromatography-mass spectrometry/mass spectrometry (LC-MS/MS) method to measure simplexin concentrations in pimelea plant material. Simplexin was quantified by positive-ion atmospheric pressure chemical ionization (APCI) LC-MS/MS with selected reaction monitoring (SRM) of the m/z 533.3 > 253.3 transition. LC-MS/MS analysis of the four poisonous taxa P. trichostachya, P. elongata, P. simplex subsp. continua, and P. simplex subsp. simplex showed similar profiles with simplexin as the major diterpenoid ester component in all four taxa accompanied by varying amounts of related orthoesters. Similar analyses of P. decora, P. haematostachya, and P. microcephala also demonstrated the presence of simplexin in these species but at far lower concentrations, consistent with the limited reports of stock poisoning associated with these species. The less common, shrubby species P. penicillaris contained simplexin at up to 55 mg/kg dry weight and would be expected to cause poisoning if animals consumed sufficient plant material.

DNA-based detection and characterisation of strictly anaerobic beer-spoilage bacteria

Megasphaera cerevisiae, Pectinatus cerevisiiphilus, Pectinatus frisingensis, Selenomonas lacticifex, Zymophilus paucivorans and Zymophilus raffinosivorans are strictly anaerobic Gram-stain-negative bacteria that are able to spoil beer by producing off-flavours and turbidity. They have only been isolated from the beer production chain. The species are phylogenetically affiliated to the Sporomusa sub-branch in the class "Clostridia". Routine cultivation methods for detection of strictly anaerobic bacteria in breweries are time-consuming and do not allow species identification. The main aim of this study was to utilise DNA-based techniques in order to improve detection and identification of the Sporomusa sub-branch beer-spoilage bacteria and to increase understanding of their biodiversity, evolution and natural sources. Practical PCR-based assays were developed for monitoring of M. cerevisiae, Pectinatus species and the group of Sporomusa sub-branch beer spoilers throughout the beer production process. The developed assays reliably differentiated the target bacteria from other brewery-related microbes. The contaminant detection in process samples (10 1,000 cfu/ml) could be accomplished in 2 8 h. Low levels of viable cells in finished beer (≤10 cfu/100 ml) were usually detected after 1 3 d culture enrichment. Time saving compared to cultivation methods was up to 6 d. Based on a polyphasic approach, this study revealed the existence of three new anaerobic spoilage species in the beer production chain, i.e. Megasphaera paucivorans, Megasphaera sueciensis and Pectinatus haikarae. The description of these species enabled establishment of phenotypic and DNA-based methods for their detection and identification. The 16S rRNA gene based phylogenetic analysis of the Sporomusa sub-branch showed that the genus Selenomonas originates from several ancestors and will require reclassification. Moreover, Z. paucivorans and Z. raffinosivorans were found to be in fact members of the genus Propionispira. This relationship implies that they were carried to breweries along with plant material. The brewery-related Megasphaera species formed a distinct sub-group that did not include any sequences from other sources, suggesting that M. cerevisiae, M. paucivorans and M. sueciensis may be uniquely adapted to the brewery ecosystem. M. cerevisiae was also shown to exhibit remarkable resistance against many brewery-related stress conditions. This may partly explain why it is a brewery contaminant. This study showed that DNA-based techniques provide useful tools for obtaining more rapid and specific information about the presence and identity of the strictly anaerobic spoilage bacteria in the beer production chain than is possible using cultivation methods. This should ensure financial benefits to the industry and better product quality to customers. In addition, DNA-based analyses provided new insight into the biodiversity as well as natural sources and relations of the Sporomusa sub-branch bacteria. The data can be exploited for taxonomic classification of these bacteria and for surveillance and control of contaminations.

Effect of Increasing Low Dose Simplexin Exposure in Cattle consuming Pimelia trychostachya

Pimelea species (or desert riceflower) are small native plants endemic to the drier inland pastoral regions of Australia, which cause a unique syndrome in grazing cattle characterised by submandibular oedema and oedema in the brisket area as a result of right-sided heart failure attributed to the toxin simplexin. Field evidence suggests that poisoning can occur through minor, inadvertent consumption of Pimelea plant material, but the minimum simplexin intake required to induce Pimelea poisoning is not known. In this study, mild Pimelea poisoning was induced at a daily dose of 12.5 mg Pimelea/kg bodyweight per day, equivalent to 2.5 µg simplexin/kg bodyweight per day, demonstrating the high potential toxicity of these plant species. Effects in all animals diminished with prolonged low dose feeding and we postulate that these animals developed mechanisms for detoxifying simplexin, 1, possibly through rumen bacteria adaptation or activation of liver enzymes.

Cotton root systems and recovery of applied P and K fertilisers

With potential to accumulate substantial amounts of above-ground biomass, at maturity an irrigated cotton crop can have taken up more than 20 kg/ha phosphorus and often more than 200 kg/ha of potassium. Despite the size of plant accumulation of P and K, recovery of applied P and K fertilisers by the crop in our field experiment program has poor. Processing large amounts of mature cotton plant material to provide a representative sample for chemical analysis has not been without its challenges, but the questions regarding mechanism of where, how and when the plant is acquiring immobile nutrients remain. Dry matter measured early in the growing season (squaring, first white flower) have demonstrated a 50% increase in crop biomass to applied P (in particular), but it represents only 20% of the total P accumulation by the plant. By first open boll (and onwards), no response in dry matter or P concentration could be detected to P application. A glasshouse study indicated P recovery was greater (to FOB) where it was completely mixed through a profile as opposed to a banded application method suggesting cotton prefers a more diffuse distribution. The relative effects of root morphology, mycorrhizal fungi infection, seasonal growth patterns and how irrigation is applied are areas for future investigation on how, when and where cotton acquires immobile nutrients.

Identification of the fungal catabolic D-galacturonate pathway

Pectin is a natural polymer consisting mainly of D-galacturonic acid monomers. Microorganisms living on decaying plant material can use D-galacturonic acid for growth. Although bacterial pathways for D-galacturonate catabolism had been described previously, no eukaryotic pathway for D-galacturonate catabolism was known at the beginning of this work. The aim of this work was to identify such a pathway. In this thesis the pathway for D-galacturonate catabolism was identified in the filamentous fungus Trichoderma reesei. The pathway consisted of four enzymes: NADPH-dependent D-galacturonate reductase (GAR1), L-galactonate dehydratase (LGD1), L-threo-3-deoxy-hexulosonate aldolase (LGA1) and NADPH-dependent glyceraldehyde reductase (GLD1). In this pathway D-galacturonate was converted to pyruvate and glycerol via L-galactonate, L-threo-3-deoxy-hexulosonate and L-glyceraldehyde. The enzyme activities of GAR1, LGD1 and LGA1 were present in crude mycelial extract only when T. reesei was grown on D-galacturonate. The activity of GLD1 was equally present on all the tested carbon sources. The corresponding genes were identified either by purifying and sequencing the enzyme or by expressing genes with homology to other similar enzymes in a heterologous host and testing the activities. The new genes that were identified were expressed in Saccharomyces cerevisiae and resulted in active enzymes. The GAR1, LGA1 and GLD1 were also produced in S. cerevisiae as active enzymes with a polyhistidine-tag, and purified and characterised. GAR1 and LGA1 catalysed reversible reactions, whereas only the forward reactions were observed for LGD1 and GLD1. When gar1, lgd1 or lga1 was deleted in T. reesei the deletion strain was unable to grow with D-galacturonate as the only carbon source, demonstrating that all the corresponding enzymes were essential for D-galacturonate catabolism and that no alternative D-galacturonate pathway exists in T. reesei. A challenge for biotechnology is to convert cheap raw materials to useful and more valuable products. Filamentous fungi are especially useful for the conversion of pectin, since they are efficient producers of pectinases. Identification of the fungal D-galacturonate pathway is of fundamental importance for the utilisation of pectin and its conversion to useful products.