Microorganisms, Australia and the Convention on Biological Diversity

The Convention on Biological Diversity arose as an international agreement for the conservation and continued exploitation of Earth's biological diversity (biodiversity). It directly affects those involved in conservation, exploitation and investigation of biodiversity in all its forms, as well as affecting the viability of all life. Australia is one of more than 170 countries that have ratified the Convention. Its involvement in this Convention will be considered in terms of the National Strategy for the Conservation of Biological Diversity with a focus on the coverage of microorganisms within this strategy. Microorganisms represent a major part of the biodiversity on Earth but, as yet, remain relatively unknown. Among those microorganisms that have been described, many, originating from a range of countries, have been deposited in culture collections worldwide. The Convention contains articles that impact on ex situ collections, although precise protocols are not set out therein. An international code of conduct is now being formulated to ensure ongoing access to and exchange of microorganisms in the interests of sustainable development in industrialised and developing nations.     

Mobile gene cassettes: a fundamental resource for bacterial evolution

Horizontal gene transfer increases genetic diversity in prokaryotes to a degree not allowed by the limitations of reproduction by binary fission. The integron/gene cassette system is one of the most recently characterized examples of a system that facilitates horizontal gene transfer. This system, discovered in the context of multidrug resistance, is recognized in a clinical context for its role in allowing pathogens to adapt to the widespread use of antibiotics. Recent studies suggest that gene cassettes are common and encode functions relevant to many adaptive traits. To estimate the diversity of mobile cassettes in a natural environment, a molecular technique was developed to provide representative distributions of cassette populations at points within a sampling area. Subsequently, statistical methods analogous to those used for calculating species diversity were employed to assess the diversity of gene cassettes within the sample area in addition to gaining an estimate of cassette pool size. Results indicated that the number of cassettes within a 5x10-m sample area was large and that the overall mobile cassette metagenome was likely to be orders of magnitude larger again. Accordingly, gene cassettes appear to be capable of mobilizing a significant genetic resource and consequently have a substantial impact on bacterial adaptability.     

Are Ethnic and Gender Specific Equations Needed to Derive Fat Free Mass from Bioelectrical Impedance in Children of South Asian,Black African-Caribbean and White European Origin? Results of the Assessment of Body Composition in Children Study

Background

Bioelectrical impedance analysis (BIA) is a potentially valuable method for assessing lean mass and body fat levels in children from different ethnic groups. We examined the need for ethnic- and gender-specific equations for estimating fat free mass (FFM) from BIA in children from different ethnic groups and examined their effects on the assessment of ethnic differences in body fat.

Methods

Cross-sectional study of children aged 8–10 years in London Primary schools including 325 South Asians, 250 black African-Caribbeans and 289 white Europeans with measurements of height, weight and arm-leg impedance (Z; Bodystat 1500). Total body water was estimated from deuterium dilution and converted to FFM. Multilevel models were used to derive three types of equation {A: FFM = linear combination(height+weight+Z); B: FFM = linear combination(height²/Z); C: FFM = linear combination(height²/Z+weight)}.

Results

Ethnicity and gender were important predictors of FFM and improved model fit in all equations. The models of best fit were ethnicity and gender specific versions of equation A, followed by equation C; these provided accurate assessments of ethnic differences in FFM and FM. In contrast, the use of generic equations led to underestimation of both the negative South Asian-white European FFM difference and the positive black African-Caribbean-white European FFM difference (by 0.53 kg and by 0.73 kg respectively for equation A). The use of generic equations underestimated the positive South Asian-white European difference in fat mass (FM) and overestimated the positive black African-Caribbean-white European difference in FM (by 4.7% and 10.1% respectively for equation A). Consistent results were observed when the equations were applied to a large external data set.

Conclusions

Ethnic- and gender-specific equations for predicting FFM from BIA provide better estimates of ethnic differences in FFM and FM in children, while generic equations can misrepresent these ethnic differences.     

Phenotypic and genetic characterization of Paecilomyces lilacinus strains with biocontrol activity against root-knot nematodes

Efficient selection of fungi for biological control of nematodes requires a series of screening assays. Assessment of genetic diversity in the candidate species maximizes the variety of the isolates tested and permits the assignment of a particular genotype with high nematophagous potential using a rapid novel assay. Molecular analyses also facilitate separation between isolates, allowing the identification of proprietary strains and trace biocontrol strains in the environment. The resistance of propagules to UV radiation is an important factor in the survival of a biocontrol agent. We have analyzed 15 strains of the nematophagous fungus Paecilomyces lilacinus using these principles. Arbitrarily primed DNA and allozyme assays were applied to place the isolates into genetic clusters, and demonstrated that some genetically related P. lilacinus strains exhibit widespread geographic distributions. When exposed to UV radiation, some weakly nematophagous strains were generally more susceptible than effective isolates. A microtitre tray-based assay used to screen the pathogenic activity of each isolate to Meloidogyne javanica egg masses revealed that the nematophagous ability varied between 37%-100%. However, there was no clear relationship between nematophagous ability and genetic clusters. Molecular characterizations revealed sufficient diversity to allow tracking of strains released into the environment.     

Winter availability of cereal stubbles attracts declining farmland birds and positively influences breeding population trends

Many studies have demonstrated the selection of stubble fields by farmland birds in winter, but none have shown whether provisioning of this key habitat positively influences national population trends for widespread farmland birds. We use two complementary extensive bird surveys undertaken at the same localities in summer and winter and show that the area of stubble in winter attracts increased numbers of several bird species of conservation concern. Moreover, for several farmland specialists, the availability of stubble fields in winter positively influenced the 10 year breeding population trend (1994-2003) whereas hedgerow bird species were less affected. For skylarks and yellowhammers, initially negative trends showed recovery with 10-20 ha of stubble per 1 km square. Thus, agri-environment schemes that promote retention of over-winter stubbles will attract birds locally and are capable of reversing current population declines if stubbles are available in sufficient quantity.     

Quantification of class 1 integron abundance in natural environments using real-time quantitative PCR

Integrons are bacterial genetic elements capable of capturing and expressing potentially adaptive genetic material. Class 1 integrons constitute the most intensely studied group of these elements to date, mainly due to their well-established role in the acquisition and dissemination of antibiotic resistance genes in clinical environments. However, virtually nothing is known about the distribution or abundance of class 1 integrons outside of the clinical context. Here we develop a SYBR Green-based real-time quantitative PCR assay capable of quantifying the abundance of class 1 integrons in environmental samples. It was shown that the abundance of the intI1 gene in creek sediment correlates with ecological condition, implying that class 1 integrons provide selective advantages relevant to environmental pressures other than the use of antibiotics. By comparing the quantities of intI1 and 16S rRNA gene in each sample, it was demonstrated that approximately 2.7% of cells potentially harbour a class 1 integron. These findings suggest that class 1 integrons are widespread in natural environments removed from clinical settings and occur in a broader range of host organisms than had previously been assumed on the basis of culture-dependent estimates.