Effect of abattoir and cut on variations in microbial communities of vacuum-packaged beef.

This report builds on the earlier studies of the shelf-life of chilled Australian vacuum packaged (VP) beef primals (striploin and cube roll), products distinguished in the global marketplace for unusually long shelf-life. Notable findings in those studies were a shelf-life of at least 26weeks at -0.5°C, low microbial counts, and relatively high sensory scores. However, growth rates for total viable counts (TVC) and lactic acid bacteria (LAB) varied among the different abattoirs. The present study adds to these findings, by providing greater definition about temporal changes in bacterial communities using terminal restriction fragment length polymorphism (TRFLP) and clone library analyses of 16S ribosomal RNA (16S rRNA) gene, and measuring statistical associations among abattoir, beef cut, storage time and sensory attributes. Bacterial communities changed over time, with Carnobacterium spp. typically predominating (29-97%) at the end of storage. Variation in TRFLP profiles showed that different Carnobacterium strains predominated in different abattoirs, and that additional variation was due to the presence of other taxa typical of VP meat microbiomes. TRFLP-based community structure correlated significantly (P≤0.01) with sensorial characteristics, such as vacuum integrity, confinement odour, and intact pack appearance of beef. This study shows that Carnobacterium spp. predominate on extended shelf-life VP beef primals, while other taxa may produce subtle effects on shelf-life duration.

Multiplex RT-PCR detection of three common viruses infecting orchids.

A multiplex reverse transcription polymerase chain reaction (RT-PCR) assay was developed for simultaneous detection of three orchid viruses: cymbidium mosaic virus (CymMV), odontoglossum ringspot virus (ORSV), and orchid fleck virus (OFV). Primers were used to amplify nucleocapsid protein gene fragments of 845 bp (ORSV), 505 bp (CymMV) and 160 bp (OFV). A 60-bp amplicon of plant glyceraldehyde-3-phophate dehydrogenase mRNA was included as an internal control against false negatives. The assay was validated against 31 collected plants from six orchid genera and compared with results obtained by transmission electron microscopy (TEM). The RT-PCR assay proved more sensitive than TEM for detection of OFV.

Comparative assessment of genetic and epigenetic variation among regenerants of potato (Solanum tuberosum) derived from long-term nodal tissue-culture and cell selection.

Three long-term nodal tissued cultured Russet Burbank potato clones and nine thaxtomin A-treated regenerant lines, derived from the nodal lines, were assessed for genetic and epigenetic (in the form of DNA methylation) differences by AFLP and MSAP. The treated regenerant lines were originally selected for superior resistance to common scab disease and acceptable tuber yield in pot and field trials. The long-term, tissue culture clone lines exhibited genetic (8.75-15.63% polymorphisms) and epigenetic (12.56-26.13% polymorphisms) differences between them and may represent a stress response induced by normal plant growth disruption. The thaxtomin A-treated regenerant lines exhibited much higher significant (p < 0.05) genetic (2-29.38%) and epigenetic (45.22-51.76%) polymorphisms than the nodal cultured parent clones. Methylation-sensitive mutations accumulated within the regenerant lines are significantly correlated (p < 0.05) to disease resistance. However, linking phenotypic differences that could be of benefit to potato growers, to single gene sequence polymorphisms in a tetraploid plant such as the potato would be extremely difficult since it is assumed many desirable traits are under polygenic control.

Investigation and optimization of a passively operated compost-based system for remediation of acidic, highly iron- and sulfate-rich industrial waste water.

A passively operated multi-stage bioremediation system utilizing composted agricultural waste products and an artificial wetland system was found to be effective for purification of acidic, iron- and sulfate-rich waste water derived from titanium mineral processing. The main microbial players involved in the remediation system processes and the dynamics were investigated; mineral processing waste water-filled sludge dams possessed stable microbial communities that included Acidithiobacillus, Desulfurella, and acidophilic, anaerobic fermenters of the order Bacteroidales. These groups were enriched in a subsequent potato waste-based iron mobilization pre-treatment stage. Within downstream reduction treatment stages ("reduction cells"), compost/straw decomposition and associated sulfur/sulfate and iron reduction were carried out by a complex mix of aerobic and anaerobic bacteria. The efficaciousness of the system without replacement of the compost was found to steadily decline following 2 years of operation and corresponded with the reduction cell communities becoming simultaneously more diverse and homogenous. Microcosm-based experiments demonstrated that operational declines were due to unsustained supply of suitable labile carbon sources combined with spatial heterogeneity within the layered design of the reduction stage of the system resulting in inadequate redox conditions. Temperature was not found to be a critical performance factor in the range of 10-25 degrees C. Application of a combined emulsified oil/molasses amendment was found to be highly effective in promoting a microbial community capable of remediating waste water with high iron and sulfate levels. Acidophilic members of the order Bacteroidales were found to be critical in the investigated remediation system, providing organic donors for subsequent metal and sulfur transformations and could have a broader ecological significance than previously suspected.