Toxoplasmosis in Indo-Pacific humpbacked dolphins (Sousa chinensis) from Queensland

Objective: To describe the clinical signs, gross pathology, serology, bacteriology, histopathology, electron microscopy and immunohistochemistry findings associated with toxoplasmosis in four Indo-Pacific humpbacked dolphins (Sousa chinensis) that stranded in Queensland in 2000 and 2001. Design: Clinical assessment, gross necropsy, and laboratory examinations. Procedure: Necropsies were performed on four S chinensis to determine cause of death. Laboratory tests including serology, bacteriology, histopathology and transmission electron microscopy were done on the four dolphins. lmmunohistochemistry was done on the brain, heart, liver, lung, spleen and adrenal gland from various dolphins to detect Toxoplasma gondii antigens. Results: Necropsies showed all of four S chinensis that stranded in Queensland in 2000 and 2001 had evidence of predatory shark attack and three were extremely emaciated. Histopathological examinations showed all four dolphins had toxoplasmosis with tissue cysts resembling T gondii in the brain. Tachyzoite stages of T gondii were detected in the lungs, heart, liver, spleen and adrenal gland, variously of all four dolphins. Electron microscopy studies and immunohistochemistry confirmed the tissues cysts were those of Tgondii. All four dolphins also had intercurrent disease including pneumonia, three had peritonitis and one had pancreatitis. Conclusion: Four S chinensis necropsied in Queensland in 2000 and 2001 were found to be infected with toxoplasmosis. It is uncertain how these dolphins became infected and further studies are needed to determine how S chinensis acquire toxoplasmosis. All four dolphins stranded after periods of heavy rainfall, and coastal freshwater runoff may be a risk factor for T gondii infection in S chinensis. This disease should be of concern to wildlife managers since S chinensis is a rare species and its numbers appear to be declining.

Ruminococcus bromii, identification and isolation as a dominant community member in the rumen of cattle fed a barley diet

Aims: To identify dominant bacteria in grain (barley)-fed cattle for isolation and future use to increase the efficiency of starch utilization in these cattle. Methods and Results: Total DNA was extracted from samples of the rumen contents from eight steers fed a barley diet for 9 and 14 days. Bacterial profiles were obtained using denaturing gradient gel electrophoresis (DGGE) of the PCR-amplified V2/V3 region of the 16S rRNA genes from total bacterial DNA. Apparently dominant bands were excised and cloned, and the clone insert sequence was determined. One of the most common and dominant bacteria present was identified as Ruminococcus bromii. This species was subsequently isolated using traditional culture-based techniques and its dominance in the grain-fed cattle was confirmed using a real-time Taq nuclease assay (TNA) designed for this purpose. In some animals, the population of R. bromii reached densities above 1010R. bromii cell equivalents per ml or approximately 10% of the total bacterial population. Conclusions: Ruminococcus bromii is a dominant bacterial population in the rumen of cattle fed a barley-based diet. Significance and Impact of the Study: Ruminococcus bromii YE282 may be useful as a probiotic inoculant to increase the efficiency of starch utilization in barley-fed cattle. The combination of DGGE and real-time TNA has been an effective process for identifying and targeting for isolation, dominant bacteria in a complex ecosystem.

Woody plant responses to various clearing strategies imposed on a poplar box (Eucalyptus populnea) community at Dingo in central Queensland

The efficacy of individual tree treatment (stem-injection), aerially applied root-absorbed herbicide and mechanical felling (with and without subsequent fire) in controlling woody plants was compared in a poplar box (Eucalyptus populnea) woodland community in central Queensland, Australia. All treatments reduced woody plant populations and basal area relative to the untreated control. Chemical control and 'mechanical felling plus fire' treatments were equally effective in reducing woody plant basal area 7 years after the treatments were imposed. However, mechanical felling alone was less effective. There was a clear tendency for the scattered tree (80% thinning) treatment to recover woody plant basal area towards pre-treatment levels faster than other clearing strategies, although this response was not significantly different from 20% clump retention and mechanical felling (without burning) treatments.

The effect of foliar sprays of the synthetic auxin 3-5-6 TPA, on fruit drop, fruit size and seed development in three lychee (Litchi chinensis) cultivars: Tai So, Fay Zee Sui and Kwai Mai Pink.

Fruit drop in lychee can cause major yield losses in Australia, the severity varying with cultivar and season. Research in China, South Africa and Israel has demonstrated the potential for synthetic auxins used as foliar sprays to reduce fruit drop in lychee. Trials were initiated in Australia to test the efficacy of the synthetic auxin, 3-5-6 Trichloro-2-phridyl-oxyacetic acid (3-5-6 TPA) at 50 ppm on the cultivars Tai So, Fay Zee Sui and Kwai Mai Pink. Results indicate that in most cases the TPA reduced natural fruit drop however the size of the fruit at the time of application affects the response and the ideal application time varies with cultivar; approximately 13 mm fruit length in 'Kwai Mai Pink', 20 mm in 'Fay Zee Sui' and 27 mm in 'Tai So'. If applied too early in 'Tai So', it caused an increase in fruit drop. The TPA was most effective when natural fruit drop was high, reducing fruit drop from 74.7 to 34.9% in 'Kwai Mai Pink' and least effective when natural fruit drop was low. An increase in the percentage of fruit with poorly developed (chicken tongue) seed and slightly larger fruit size was also observed in treated trees.

Impact of tillage and residues from rotation crops on the nematode community in soil and surface mulch during the following sugarcane crop.

The impact of three cropping histories (sugarcane, maize and soybean) and two tillage practices (conventional tillage and direct drill) on plant-parasitic and free-living nematodes in the following sugarcane crop was examined in a field trial at Bundaberg. Soybean reduced populations of lesion nematode (Pratylenchus zeae) and root-knot nematode (Meloidogyne javanica) in comparison to previous crops of sugarcane or maize but increased populations of spiral nematode (Helicotylenchus dihystera) and maintained populations of dagger nematode (Xiphinema elongatum). However the effect of soybean on P zeae and M. javanica was no longer apparent 15 weeks after planting sugarcane, while later in the season, populations of these nematodes following soybean were as high as or higher than maize or sugarcane. Populations of P zeae were initially reduced by cultivation but due to strong resurgence tended to be higher in conventionally tilled than direct drill plots at the end of the plant crop. Even greater tillage effects were observed with M. javanica and X. elongatum, as nematode populations were significantly higher in conventionally tilled than direct drill plots late in the season. Populations of free-living nematodes in the upper 10 cm of soil were initially highest following soybean, but after 15, 35 and 59 weeks were lower than after sugarcane and contained fewer omnivorous and predatory nematodes. Conventional tillage increased populations of free-living nematodes in soil in comparison to direct drill and was also detrimental to omnivorous and predatory nematodes. These results suggest that crop rotation and tillage not only affect plant-parasitic nematodes directly, but also have indirect effects by impacting on natural enemies that regulate nematode populations. More than 2 million nematodes/m(2) were often present in crop residues on the surface of direct drill plots. Bacterial-feeding nematodes were predominant in residues early in the decomposition process but fungal-feeding nematodes predominated after 15 weeks. This indicates that fungi become an increasingly important component of the detritus food web as decomposition proceeds, and that that the rate of nutrient cycling decreases with time. Correlations between total numbers of free-living nematodes and mineral N concentrations in crop residues and surface soil suggested that the free-living nematode community may provide an indication of the rate of mineralisation of N from organic matter.

Development of a Gulf community based natural resource monitoring program.

Development of a Gulf community based natural resource monitoring program, with sawfish as an initial focus.

Traffic tolerance of warm season turfgrasses under Community Sportsfield Conditions

The four-year Horticulture Australia (HAL) project is the first scientific study within Australia to assess simulated and actual wear studies of warm-season turfgrasses suitable for sportfield use. The study has allowed researchers and turf professionals to compare traffic (wear and compaction) tolerance and turf management requirements (e.g. mowing) of the current dominant varieties.

Bacterial Community Structure in the Hindgut of Wild and Captive Dugongs (Dugong dugon)

Dugongs (Dugong dugon) are marine mammals that obtain nutrients through hindgut fermentation of seagrass, however, the microbes responsible have not been identified. This study used denaturing gradient gel electrophoresis (DGGE) and 454-pyrosequencing to profile hindgut bacterial communities in wild dugongs. Faecal samples obtained from 32 wild dugongs representing four size/maturity classes, and two captive dugongs fed on cos lettuce were screened using DGGE. Partial 16S rRNA gene profiles of hindgut bacteria from wild dugong calves and juveniles were grouped together and were different to those in subadults and adults. Marked differences between hindgut bacterial communities of wild and captive dugongs were also observed, except for a single captive whose profile resembled wild adults following an unsuccessful reintroduction to the wild. Pyrosequencing of hindgut communities in two wild dugongs confirmed the stability of bacterial populations, and Firmicutes (average 75.6% of Operational Taxonomic Units [OTUs]) and Bacteroidetes (19.9% of OTUs) dominated. Dominant genera were Roseburia, Clostridium, and Bacteroides. Hindgut microbial composition and diversity in wild dugongs is affected by ontogeny and probably diet. In captive dugongs, the absence of the dominant bacterial DNA bands identified in wild dugongs is probably dependent upon prevailing diet and other captive conditions such as the use of antibiotics. This study represents a first step in the characterisation of a novel microbial ecosystem-the marine hindgut of Sirenia.

Shedding Light on the Microbial Community of the Macropod Foregut Using 454-Amplicon Pyrosequencing

Twenty macropods from five locations in Queensland, Australia, grazing on a variety of native pastures were surveyed and the bacterial community of the foregut was examined using 454-amplicon pyrosequencing. Specifically, the V3/V4 region of 16S rRNA gene was examined. A total of 5040 OTUs were identified in the data set (post filtering). Thirty-two OTUs were identified as 'shared' OTUS (i.e. present in all samples) belonging to either Firmicutes or Bacteroidetes (Clostridiales/Bacteroidales). These phyla predominated the general microbial community in all macropods. Genera represented within the shared OTUs included: unclassified Ruminococcaceae, unclassified Lachnospiraceae, unclassified Clostridiales, Peptococcus sp. Coprococcus spp., Streptococcus spp., Blautia sp., Ruminoccocus sp., Eubacterium sp., Dorea sp., Oscillospira sp. and Butyrivibrio sp. The composition of the bacterial community of the foregut samples of each the host species (Macropus rufus, Macropus giganteus and Macropus robustus) was significantly different allowing differentiation between the host species based on alpha and beta diversity measures. Specifically, eleven dominant OTUs that separated the three host species were identified and classified as: unclassified Ruminococcaceae, unclassified Bacteroidales, Prevotella spp. and a Syntrophococcus sucromutans. Putative reductive acetogens and fibrolytic bacteria were also identified in samples. Future work will investigate the presence and role of fibrolytics and acetogens in these ecosystems. Ideally, the isolation and characterization of these organisms will be used for enhanced feed efficiency in cattle, methane mitigation and potentially for other industries such as the biofuel industry.

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.

Morphological and molecular diversity of Colletotrichum spp. causing pepper spot and anthracnose of lychee (Litchi chinensis) in Australia

Since the 1980s a new disease has been affecting Australian lychee. Pepper spot appears as small, black superficial lesions on fruit, leaves, petioles and pedicels and is caused by Colletotrichum gloeosporioides, the same fungus that causes postharvest anthracnose of lychee fruit. The aim of this study was to determine if a new genotype of C.gloeosporioides is responsible for the pepper spot symptom. Morphological assessments, arbitrarily-primed PCR (ap-PCR) and DNA sequencing studies did not differentiate isolates of C.gloeosporioides from anthracnose and pepper spot lesions. The ap-PCR identified 21 different genotypes of C.gloeosporioides, three of which were predominant. A specific genotype identified using ap-PCR was associated with the production of the teleomorph in culture. Analysis of sequence data of ITS and -tubulin regions of representative isolates did not group the lychee isolates into a monophyletic clade; however, given the majority of the isolates were from one of three genotypes found using ap-PCR, the possibility of a lychee specific group of C.gloeosporioides is discussed.

Microbial indicators related to yield and disease and changes in soil microbial community structure with ginger farm management practices

TRFLP (terminal restriction fragment length polymorphism) was used to assess whether management practices that improved disease suppression and/or yield in a 4-year ginger field trial were related to changes in soil microbial community structure. Bacterial and fungal community profiles were defined by presence and abundance of terminal restriction fragments (TRFs), where each TRF represents one or more species. Results indicated inclusion of an organic amendment and minimum tillage increased the relative diversity of dominant fungal populations in a system dependant way. Inclusion of an organic amendment increased bacterial species richness in the pasture treatment. Redundancy analysis showed shifts in microbial community structure associated with different management practices and treatments grouped according to TRF abundance in relation to yield and disease incidence. ANOVA also indicated the abundance of certain TRFs was significantly affected by farming system management practices, and a number of these TRFs were also correlated with yield or disease suppression. Further analyses are required to determine whether identified TRFs can be used as general or soil-type specific bio-indicators of productivity (increased and decreased) and Pythium myriotylum suppressiveness.

The water relations and irrigation requirements of lychee (litchi chinensis sonn.): a review

The results of research into the water relations and irrigation requirements of lychee are collated and reviewed. The stages of plant development are summarised, with an emphasis on factors influencing the flowering process. This is followed by reviews of plant water relations, water requirements, water productivity and, finally, irrigation systems. The lychee tree is native to the rainforests of southern China and northern Vietnam, and the main centres of production remain close to this area. In contrast, much of the research on the water relations of this crop has been conducted in South Africa, Australia and Israel where the tree is relatively new. Vegetative growth occurs in a series of flushes. Terminal inflorescences are borne on current shoot growth under cool (<15 °C), dry conditions. Trees generally do not produce fruit in the tropics at altitudes below 300 m. Poor and erratic flowering results in low and irregular fruit yields. Drought can enhance flowering in locations with dry winters. Roots can extract water from depths greater than 2 m. Diurnal trends in stomatal conductance closely match those of leaf water status. Both variables mirror changes in the saturation deficit of the air. Very little research on crop water requirements has been reported. Crop responses to irrigation are complex. In areas with low rainfall after harvest, a moderate water deficit before floral initiation can increase flowering and yield. In contrast, fruit set and yield can be reduced by a severe water deficit after flowering, and the risk of fruit splitting increased. Water productivity has not been quantified. Supplementary irrigation in South-east Asia is limited by topography and competition for water from the summer rice crop, but irrigation is practised in Israel, South Africa, Australia and some other places. Research is needed to determine the benefits of irrigation in different growing areas. Copyright © Cambridge University Press 2013.

Can soil nematode community structure be used to indicate soil carbon dynamics in horticultural systems?

There is a need to develop indicators that relate the dynamics of soil organic carbon (SOC) with changes in land management of horticultural production systems. Soil nematode communities have been shown to be sensitive to land management changes, but often do not include plant-parasites in the calculation of soil nematode community indices. The concept of nematode functional guilds was used to estimate the proportion of carbon entering the soil ecosystem through different channels, such as through decomposition of organic material, the detrital channel, through the roots of plants, the root channel or recycled through the activity of predators, a predation channel. Calculations of the indices were developed and validated using case studies in the north Queensland banana industry. Firstly, a survey of organic and conventional banana farms found a greater proportion of C entering the soil ecosystem through the detrital channel and a reduced proportion of C originating through the root channel at the organic sites relative to conventional sites. Secondly, a field experiment comparing compost amendments, found application of fresh compost significantly increased the proportion of C entering the soil ecosystem through the detrital channel and decreased proportion of C originating from the root channel. Thirdly, a field experiment comparing 'conventional' banana production to an 'alternative' system which incorporated organic matter, found the proportion of C entering the soil ecosystem through the root channel was significantly greater in the conventional systems relative to the alternative system. This research demonstrates that nematode indices can be used to assess horticultural systems, by indicating the origins of SOC.

Fungal community structure in disease suppressive soils assessed by 28S LSU gene sequencing

Natural biological suppression of soil-borne diseases is a function of the activity and composition of soil microbial communities. Soil microbe and phytopathogen interactions can occur prior to crop sowing and/or in the rhizosphere, subsequently influencing both plant growth and productivity. Research on suppressive microbial communities has concentrated on bacteria although fungi can also influence soil-borne disease. Fungi were analyzed in co-located soils 'suppressive' or 'non-suppressive' for disease caused by Rhizoctonia solani AG 8 at two sites in South Australia using 454 pyrosequencing targeting the fungal 28S LSU rRNA gene. DNA was extracted from a minimum of 125 g of soil per replicate to reduce the micro-scale community variability, and from soil samples taken at sowing and from the rhizosphere at 7 weeks to cover the peak Rhizoctonia infection period. A total of ∼994,000 reads were classified into 917 genera covering 54% of the RDP Fungal Classifier database, a high diversity for an alkaline, low organic matter soil. Statistical analyses and community ordinations revealed significant differences in fungal community composition between suppressive and non-suppressive soil and between soil type/location. The majority of differences associated with suppressive soils were attributed to less than 40 genera including a number of endophytic species with plant pathogen suppression potentials and mycoparasites such as Xylaria spp. Non-suppressive soils were dominated by Alternaria , Gibberella and Penicillum. Pyrosequencing generated a detailed description of fungal community structure and identified candidate taxa that may influence pathogen-plant interactions in stable disease suppression. © 2014 Penton et al.