Bacterial and fungal community composition over time in chicken litter with high or low moisture content

1. Changes in bacterial and fungal communities in chicken litter with high and low moisture content over a five week period during a single chicken grow out cycle in a poultry shed in subtropical Australia were investigated to study the association between specific microbes and odour production. 2. Microbial biomass, as indicated by DNA yields, was higher and community composition was more dynamic over time in moist compared with dry chicken litter. 3. Bacillus, Atopostipes and Aspergillus species increased in relative abundance in moist chicken litter samples over time reflecting the relatively high fitness and hence activity of these specific bacteria and this specific fungus in this environment.

Resistance to phosphine in Sitophilus oryzae in Australia: A national analysis of trends and frequencies over time and geographical spread

In Australia, along with many other parts of the world, fumigation with phosphine is a vital component in controlling stored grain insect pests. However, resistance is a factor that may limit the continued efficacy of this fumigant. While strong resistance to phosphine has been identified and characterised, very little information is available on the causes of its development and spread. Data obtained from a unique national resistance monitoring and management program were analysed, using Bayesian hurdle modelling, to determine which factors may be responsible. Fumigation in unsealed storages, combined with a high frequency of weak resistance, were found to be the main criteria that led to the development of strong resistance in Sitophilus oryzae. Independent development, rather than gene flow via migration, appears to be primarily responsible for the geographic incidence of strong resistance to phosphine in S. oryzae. This information can now be utilised to direct resources and education into those areas at high risk and to refine phosphine resistance management strategies.

Flood related loss and recovery of intertidal seagrass meadows in southern Queensland, Australia

The loss and recovery of intertidal seagrass meadows were assessed following the flood related catastrophic loss of seagrass meadows in February 1999 in the Sandy Strait, Queensland. Region wide recovery rates of intertidal meadows following the catastrophic disturbance were assessed by mapping seagrass abundance in the northern Great Sandy Strait region prior to and on 3 occasions after widespread loss of seagrass. Meadow-scale assessments of seagrass loss and recovery focussed on two existing Zostera capricorni monitoring meadows in the region. Mapping surveys showed that approximately 90% of intertidal seagrasses in the northern Great Sandy Strait disappeared after the February 1999 flooding of the Mary River. Full recovery of all seagrass meadows took 3 years. At the two study sites (Urangan and Wanggoolba Creek) the onset of Z. capricorni germination following the loss of seagrass occurred 14 months post-flood at Wanggoolba Creek, and at Urangan it took 20 months for germination to occur. By February 2001 (24 months post-flood) seagrass abundance at Wanggoolba Creek sites was comparable to pre-flood abundance levels and full recovery at Urangan sites was complete in August 2001 (31 months post-flood). Reduced water quality characterised by 2–3 fold increases in turbidity and nutrient concentrations during the 6 months following the flood was followed by a 95% loss of seagrass meadows in the region. Reductions in available light due to increased flood associated turbidity in February 1999 were the likely cause of seagrass loss in the Great Sandy Strait region, southern Queensland. Although seasonal cues influence the germination of Z. capricorni, the temporal variation in the onset of seed germination between sites suggests that germination following seagrass loss may be dependent on other factors (eg. physical and chemical characteristics of sediments and water). Elevated dissolved nitrogen concentrations during 1999 at Wanggoolba Creek suggest that this site received higher loads of sediments and nutrients from flood waters than Urangan. The germination of seeds at Wanggoolba Creek one year prior to Urangan coincides with relatively low suspended sediment concentrations in Wanggoolba Creek waters. The absence of organic rich sediments at Urangan for many months following their removal during the 1999 flood may also have inhibited seed germination. Data from population cohort analyses and population growth rates showed that rhizome weight and rhizome elongation rates increased over time, consistent with rapid growth during increases in temperature and light availability from May to October

Sustaining productivity of a Vertosol at Warra, Queensland, with fertilisers, no-tillage or legumes. 8. Effect of duration of lucerne ley on soil nitrogen and water, wheat yield and protein.

Soil nitrogen (N) supply in the Vertosols of southern Queensland, Australia has steadily declined as a result of long-term cereal cropping without N fertiliser application or rotations with legumes. Nitrogen-fixing legumes such as lucerne may enhance soil N supply and therefore could be used in lucerne-wheat rotations. However, lucerne leys in this subtropical environment can create a soil moisture deficit, which may persist for a number of seasons. Therefore, we evaluated the effect of varying the duration of a lucerne ley (for up to 4 years) on soil N increase, N supply to wheat, soil water changes, wheat yields and wheat protein on a fertility-depleted Vertosol in a field experiment between 1989 and 1996 at Warra (26degrees 47'S, 150degrees53'E), southern Queensland. The experiment consisted of a wheat-wheat rotation, and 8 treatments of lucerne leys starting in 1989 (phase 1) or 1990 (phase 2) for 1,2,3 or 4 years duration, followed by wheat cropping. Lucerne DM yield and N yield increased with increasing duration of lucerne leys. Soil N increased over time following 2 years of lucerne but there was no further significant increase after 3 or 4 years of lucerne ley. Soil nitrate concentrations increased significantly with all lucerne leys and moved progressively downward in the soil profile from 1992 to 1995. Soil water, especially at 0.9-1.2 m depth, remained significantly lower for the next 3 years after the termination of the 4 year lucerne ley than under continuous wheat. No significant increase in wheat yields was observed from 1992 to 1995, irrespective of the lucerne ley. However, wheat grain protein concentrations were significantly higher under lucerne-wheat than under wheat wheat rotations for 3-5 years. The lucerne yield and soil water and nitrate-N concentrations were satisfactorily simulated with the APSIM model. Although significant N accretion occurred in the soil following lucerne leys, in drier seasons, recharge of the drier soil profile following long duration lucerne occurred after 3 years. Consequently, 3- and 4-year lucerne-wheat rotations resulted in more variable wheat yields than wheat-wheat rotations in this region. The remaining challenge in using lucerne-wheat rotations is balancing the N accretion benefits with plant-available water deficits, which are most likely to occur in the highly variable rainfall conditions of this region.

Piggery pond sludge as a nitrogen source for crops. 1. Mineral N supply estimated from laboratory incubations and field application of stockpiled and wet sludge

Piggery pond sludge (PPS) was applied, as-collected (Wet PPS) and following stockpiling for 12 months (Stockpiled PPS), to a sandy Sodosol and clay Vertosol at sites on the Darling Downs of Queensland. Laboratory measures of N availability were carried out on unamended and PPS-amended soils to investigate their value in estimating supplementary N needs of crops in Australia's northern grains region. Cumulative net N mineralised from the long-term (30 weeks) leached aerobic incubation was described by a first-order single exponential model. The mineralisation rate constant (0.057/week) was not significantly different between Control and PPS treatments or across soil types, when the amounts of initial mineral N applied in PPS treatments were excluded. Potentially mineralisable N (No) was significantly increased by the application of Wet PPS, and increased with increasing rate of application. Application of Wet PPS significantly increased the total amount of inorganic N leached compared with the Control treatments. Mineral N applied in Wet PPS contributed as much to the total mineral N status of the soil as did that which mineralised over time from organic N. Rates of C02 evolution during 30 weeks of aerobic leached incubation indicated that the Stockpiled PPS was more stabilised (19-28% of applied organic C mineralised) than the WetPPS (35-58% of applied organic C mineralised), due to higher lignin content in the former. Net nitrate-N produced following 12 weeks of aerobic non-leached incubation was highly correlated with net nitrate-N leached during 12 weeks of aerobic incubation (R^2 = 0.96), although it was <60% of the latter in both sandy and clayey soils. Anaerobically mineralisable N determined by waterlogged incubation of laboratory PPS-amended soil samples increased with increasing application rate of Wet PPS. Anaerobically minemlisable N from field-moist soil was well correlated with net N mineralised during 30 weeks of aerobic leached incubation (R^2 =0.90 sandy soil; R^2=0.93 clay soil). In the clay soil, the amount of mineral N produced from all the laboratory incubations was significantly correlated with field-measured nitrate-N in the soil profile (0-1.5 m depth) after 9 months of weed-free fallow following PPS application. In contrast, only anaerobic mineralisable N was significantly correlated with field nitrate-N in the sandy soil. Anaerobic incubation would, therefore, be suitable as a rapid practical test to estimate potentially mineralisable N following applications of different PPS materials in the field.

Development of a stable isotope index to assess decadal-scale vegetation change and application to woodlands of the Burdekin catchment, Australia

Forty-four study sites were established in remnant woodland in the Burdekin River catchment in tropical north-east Queensland, Australia, to assess recent (decadal) vegetation change. The aim of this study was further to evaluate whether wide-scale vegetation 'thickening' (proliferation of woody plants in formerly more open woodlands) had occurred during the last century, coinciding with significant changes in land management. Soil samples from several depth intervals were size separated into different soil organic carbon (SOC) fractions, which differed from one another by chemical composition and turnover times. Tropical (C4) grasses dominate in the Burdekin catchment, and thus δ13C analyses of SOC fractions with different turnover times can be used to assess whether the relative proportion of trees (C3) and grasses (C4) had changed over time. However, a method was required to permit standardized assessment of the δ13C data for the individual sites within the 13 Mha catchment, which varied in soil and vegetation characteristics. Thus, an index was developed using data from three detailed study sites and global literature to standardize individual isotopic data from different soil depths and SOC fractions to reflect only the changed proportion of trees (C3) to grasses (C3) over decadal timescales. When applied to the 44 individual sites distributed throughout the Burdekin catchment, 64% of the sites were shown to have experienced decadal vegetation thickening, while 29% had remained stable and the remaining 7% had thinned. Thus, the development of this index enabled regional scale assessment and comparison of decadal vegetation patterns without having to rely on prior knowledge of vegetation changes or aerial photography.

An asparaginyl endopeptidase mediates in vivo protein backbone cyclization

Proteases can catalyze both peptide bond cleavage and formation, yet the hydrolysis reaction dominates in nature. This presents an interesting challenge for the biosynthesis of backbone cyclized (circular) proteins, which are encoded as part of precursor proteins and require post-translational peptide bond formation to reach their mature form. The largest family of circular proteins are the plant-produced cyclotides; extremely stable proteins with applications as bioengineering scaffolds. Little is known about the mechanism by which they are cyclized in vivo but a highly conserved Asn (occasionally Asp) residue at the C terminus of the cyclotide domain suggests that an enzyme with specificity for Asn (asparaginyl endopeptidase; AEP) is involved in the process. Nicotiana benthamiana does not endogenously produce circular proteins but when cDNA encoding the precursor of the cyclotide kalata B1 was transiently expressed in the plants they produced the cyclotide, together with linear forms not commonly observed in cyclotide-containing plants. Observation of these species over time showed that in vivo asparaginyl bond hydrolysis is necessary for cyclization. When AEP activity was suppressed, either by decreasing AEP gene expression or using a specific inhibitor, the amount of cyclic cyclotide in the plants was reduced compared with controls and was accompanied by the accumulation of extended linear species. These results suggest that an AEP is responsible for catalyzing both peptide bond cleavage and ligation of cyclotides in a single processing event.

Measuring the traction profile on sportsfields: Equipment development and testing

Traction is recognised as an important component of the overall playability and safety of a sportsfield. It relates to the "grip", or footing, provided through an athlete's shoe when in contact with the surface, and is normally measured by the torque generated when a weighted studded disc apparatus is dropped onto the turf and twisted manually. This paper describes the development of an automated traction tester, which mechanises the dropping and twisting of the weighted studded disc. By standardising these operational stages, more repeatable and reliable results can be expected than from the original hand-operated design where positioning of the disc and speed of rotation are controlled manually and so can vary from one measurement to the next. As well as measuring the maximum torque reached during rotation of the studded disc, the automated traction tester generates a profile of torque showing changes over time and calculates the angle through which the studded disc moved before reaching maximum torque. These aspects are now covered by a utility patent (PAT/AU/2004270767). Use of the automated traction tester is illustrated by comparative data for a range of warm-season turfgrasses, by comparisons of traction under different surface conditions generated by wear on Cynodon dactylon cultivars, and by the effects of environment, management and playing patterns on traction across a multi-use sports stadium.

The effect of endophyte on the performance of irrigated perennial ryegrasses in subtropical Australia

The effect of fungal endophyte (Neotyphodium lolii) infection on the performance of perennial ryegrass (Lolium perenne) growing under irrigation in a subtropical environment was investigated. Seed of 4 cultivars, infected with standard (common toxic or wild-type) endophyte or the novel endophyte AR1, or free of endophyte (Nil), was sown in pure swards, which were fertilised with 50 kg N/ha.month. Seasonal and total yield, persistence, and rust susceptibility were assessed over 3 years, along with details of the presence of endophyte and alkaloids in plant shoots. Endophyte occurrence in tillers in both the standard and AR1 treatments was above 95% for Bronsyn and Impact throughout and rose to that level in Samson by the end of the second year. Meridian AR1 only reached 93% while, in the standard treatment, the endophyte had mostly died before sowing. Nil Zendophyte treatments carried an average of ?0.6% infection throughout. Infection of the standard endophyte was associated with increased dry matter (DM) yields in all 3 years compared with no endophyte. AR1 also significantly increased yields in the second and third years. Over the full 3 years, standard and AR1 increased yields by 18% and 11%, respectively. Infection with both endophytes was associated with increased yields in all 4 seasons, the effects increasing in intensity over time. There was 27% better persistence in standard infected plants compared with Nil at the end of the first year, increasing to 198% by the end of the experiment, while for AR1 the improvements were 20 and 134%, respectively. The effect of endophyte on crown rust (Puccinia coronata) infection was inconsistent, with endophyte increasing rust damage on one occasion and reducing it on another. Cultivar differences in rust infection were greater than endophyte effects. Plants infected with the AR1 endophyte had no detectable ergovaline or lolitrem B in leaf, pseudostem, or dead tissue. In standard infected plants, ergovaline and lolitrem B were highest in pseudostem and considerably lower in leaf. Dead tissue had very low or no detectable ergovaline but high lolitrem B concentrations. Peramine concentration was high and at similar levels in leaf and pseudostem, but not detectable in dead material. Concentration was similar in both AR1 and standard infected plants. Endophyte presence appeared to have a similar effect in the subtropics as has been demonstrated in temperate areas, in terms of improving yields and persistence and increasing tolerance of plants to stress factors.

Habitat dynamics in the bed sediments of an intermittent upland stream

The effects of the hydrological regime on temporal changes to physical characteristics of substratum habitat, sediment texture of surface sediments (<10 cm), were investigated in a sub-tropical headwater stream over four years. Surface discharge was measured together with vertical hydraulic gradient and groundwater depth in order to explore features of sediment habitat that extend beyond the streambed surface. Whilst the typical discharge pattern was one of intermittent base flows and infrequent flow events associated with monsoonal rain patterns, the study period also encompassed a drought and a one-in-a-hundred-year flood. Rainfall and discharge did not necessarily reflect the actual conditions in the stream. Although surface waters were persistent long after discharge ceased, the streambed was completely dry on several occasions. Shallow groundwater was present at variable depths throughout the study period, being absent only at the height of the drought. The streambed sediments were mainly gravels, sand and clay. Finer sediment fractions showed a marked change in grain size over time, although bedload movement was limited to a single high discharge event. In response to a low discharge regimen (drought), sediments characteristically showed non-normal distributions and were dominated by finer materials. A high-energy discharge event produced a coarsening of sands and a diminished clay fraction in the streambed. Particulate organic matter from sediments showed trends of build-up and decline with the high and low discharge regimes, respectively. Within the surface sediment intersticies three potential categories of invertebrate habitat were recognised, each with dynamic spatial and temporal boundaries.

The performance of strawberry plugs in Queensland

Plugs or containerized plants can offer several advantages over traditional bare-rooted runner plants for strawberry (Fragaria x ananassa) production. Some of these benefits include easier planting, better establishment, fewer pests and diseases, and lower water use during plant establishment resulting in less leaching of applied fertilizers. Plugs also offer the potential for mechanical planting. In some areas of Europe and North America, plugs provide earlier production, greater productivity and larger fruit than runners. Research has also shown that the plants can be grown under short days and low temperatures to manipulate flower initiation and fruiting. Plugs are more expensive to buy compared with runner plants, and will only be adopted by industry if the extra costs are matched by convenience, resource conservation, increased fruiting and returns to producers. We investigated the productivity of 'Festival' and 'Sugarbaby' propagated as plugs (75 cm3 containers) and runners from Stanthorpe in southern Queensland (elevation of 872 m), and grown at Nambour on the Sunshine Coast (elevation 29 m). At planting, the plug plants weighed 0.8 ± 0.1 g DW compared with 53 ± 0.5 g DW for the runner plants. 'Sugarbaby' plugs were larger than 'Festival' plugs (33 ± 0.6 g versus 2.9 ± 0.6 g). The differences in growth at planting were maintained until the third week of July (day 94), with the plug plants weighing 17.8 ± 2.2 g, and the runner plants 21.4 ± 23 g. The proportion of plant dry matter allocated to the leaves increased over time from 59 to 70%, while the proportion allocated to the roots decreased from 21 to 10%. Harvest commenced after 60 days, with the plug plants yielding only 60% of the yields of the runner plants up until 8 August or day 109 (14.2 ± 1.4 g plant -1 week-1 versus 23.6 ± 1.9 g plant-1 week-1). 'Festival' (22.2 ± 2.0 g plant-1 week -1) had higher yields than 'Sugarbaby' (15.5 ± 1.5 g plant-1 week-1), even though plants of the latter were larger. Average fruit weight was 15.6 ± 0.3 g, with no effect of cultivar, plant type or harvest time. In other words, the differences in yield between the various treatments were due to differences in fruit set The lower yields of the plug plants probably reflect their small size at planting. Future research should determine whether plugs grown in larger cells (150 to 300 cm3 as in the USA and Europe) are more productive. Tips to be grown in larger containers should be harvested earlier than those for small cells to maximize root growth of the plug plant. This will probably extend the time required from harvest of the tips and potting them from the current four to five weeks, to eight to ten weeks.

Stakeholder expectations for environmental assurance in agriculture: Lessons from the pastoral industry

This paper outlines the expectations of a wide range of stakeholders for environmental assurance in the pastoral industries and agriculture generally. Stakeholders consulted were domestic consumers, rangeland graziers, members of environmental groups, companies within meat and wool supply chains, and agricultural industry, environmental and consumer groups. Most stakeholders were in favour of the application of environmental assurance to agriculture, although supply chains and consumers had less enthusiasm for this than environmental and consumer groups. General public good benefits were more important to environmental and consumer groups, while private benefits were more important to consumers and supply chains. The 'ideal' form of environmental assurance appears to be a management system that provides for continuous improvement in environmental, quality and food safety outcomes, combined with elements of ISO 14024 eco-labelling such as life-cycle assessment, environmental performance criteria, third-party certification, labelling and multi-stakeholder involvement. However, market failure prevents this from being implemented and will continue to do so for the foreseeable future. In the short term, members of supply chains (the people that must implement and fund environmental assurance) want this to be kept simple and low cost, to be built into their existing industry standards and to add value to their businesses. As a starting point, several agricultural industry organisations favour the use of a basic management system, combining continuous improvement, risk assessment and industry best management practice programs, which can be built on over time to meet regulator, market and community expectations.

Quantifying Transmission of Campylobacter jejuni in Commercial Broiler Flocks

Since meat from poultry colonized with Campylobacter spp. is a major cause of bacterial gastroenteritis, human exposure should be reduced by, among other things, prevention of colonization of broiler flocks. To obtain more insight into possible sources of introduction of Campylobacter into broiler flocks, it is essential to estimate the moment that the first bird in a flock is colonized. If the rate of transmission within a flock were known, such an estimate could be determined from the change in the prevalence of colonized birds in a flock over time. The aim of this study was to determine the rate of transmission of Campylobacter using field data gathered for 5 years for Australian broiler flocks. We used unique sampling data for 42 Campylobacter jejuni-colonized flocks and estimated the transmission rate, which is defined as the number of secondary infections caused by one colonized bird per day. The estimate was 2.37 +/- 0.295 infections per infectious bird per day, which implies that in our study population colonized flocks consisting of 20,000 broilers would have an increase in within-flock prevalence to 95% within 4.4 to 7.2 days after colonization of the first broiler. Using Bayesian analysis, the moment of colonization of the first bird in a flock was estimated to be from 21 days of age onward in all flocks in the study. This study provides an important quantitative estimate of the rate of transmission of Campylobacter in broiler flocks, which could be helpful in future studies on the epidemiology of Campylobacter in the field.

Will biological control of Lantana camara ever succeed? Patterns, processes & prospects

Despite biocontrol research spanning over 100 years, the hybrid weed, commonly referred to as Lantana camara, is not under adequate control. Host specificity and varietal preference of released agents, climatic suitability of a region for released agents, number of agents introduced and range or area of infestation appear to play a role in limiting biocontrol success. At least one of 41 species of mainly leaf- or flower-feeding insects has been introduced, or spread, to 41 of the 70 countries or regions where lantana occurs. Over half (26) of these species have established, achieving varying levels of herbivory and presumably some degree of control. Accurate taxonomy of the plant and adaptation of potential agents to the host plant are some of the better predictors of at least establishment success. Retrospective analysis of the hosts of introduced biocontrol agents for L. camara show that a greater proportion of agents that were collected from L. camara or Lantana urticifolia established, than agents that were collected from other species of Lantana. Of the introduced agents that had established and were oligophagous, 18 out of 22 established. The proportion of species establishing, declined with the number of species introduced. However, there was no trend when oceanic islands were treated separately from mainland areas and the result is likely an artefact of how introductions have changed over time. A calculated index of the degree of herbivory due to agents known to have caused some damage per country, was not related to land area infested with lantana for mainlands nor for oceanic islands. However, the degree of herbivory is much higher on islands than mainlands. This difference between island and mainland situations may reflect population dynamics in patchy or metapopulation landscapes. Basic systematic studies of the host remain crucial to successful biocontrol, especially of hybrid weeds like L. camara. Potential biocontrol agents should be monophages collected from the most closely related species to the target weed or be phytophages that attack several species of lantana. Suitable agents should be released in the most ideal ecoclimatic area. Since collection of biocontrol agents has been limited to a fraction of the known number of phytophagous species available, biocontrol may be improved by targeting insects that feed on stems and roots, as well as the agents that feed on leaves and flowers.