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.

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.

Archaeaphage therapy to control rumen methanogens

Phage therapy is becoming increasingly important as a means of eradicating or controlling microbial populations and has been raised as a potential strategy to reduce methane emissions from ruminants. To date, very little is currently known about phages which may infect the methane-producing archaeal strains (methanogens) dominant within the rumen of Australian cattle, such as the Methanobrevibacter ruminantium. This project aimed to assemble a collection of phages to be employed in phage therapy. A range of animal-derived and environmental source samples were tested using culture-based methodology, however no lytic phages of methanogens were isolated. Given the dearth of knowledge regarding phages of rumen methanogens, this project established that these naturally-occurring phages may be present in very low concentrations within the rumen and this will need to be considered in future methanogen-phage isolation investigations. The project has begun the process of developing and adapting new methodologies for detecting and examining these phages

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.

Gene to Phenotype Integrative Science and Modelling Applied to Pioneer elite

This project aims to use simulatiion modelling to improve our understanding of the genetics and physiology of complex traits with a view to increasing the rate of genetic gain in plant breeding programs.

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.