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Microbiology Australia Microbiology Australia
Issue 2

Vertical Transmission, May 2011

Since my last bulletin, we, the Executive, have made considerable progress in “steadying the ship”. We now have arrangements with ICMS to manage our annual conference and run our national office until the end of August next year. This has resulted in a great deal of stability for our immediate future, and we expect next year’s budget (April to March) to be back in surplus. The Executive and Council also have agreed that we will go out to tender for conference and national office management in the next few months for a fixed period from Septembe...

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Microbial systematics

This special issue of Microbiology Australia covers microbial systematics. In guest-editing this issue my intention has been to bring world experts together to discuss the past, present and future of microbial systematics with a view on the technical and theoretical advancements in the field. While the global debate continues on how to define “microbial species” in the light of recent advances, expert authors contribute insights into how sound taxonomical analyses can benefit this process of redefinition.

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Molecular taxonomic parameters

The parameters in place for the circumscription of taxonomic ranks increase with the description of lower ranks; only one or a few, mostly genomic properties, for phyla, classes and orders, while those for families, genera and, above all, for species, are described with increasing complexity, including molecular, chemotaxonomic, morphological and biochemical properties. Even the attempt to list a few examples for species-rich genera or for a phylogenetically diverse range of taxa would go beyond the scope of this communication. Rather, the pres...

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What’s up with Bergey’s?

This spring, the last volume of the 2nd edition of Bergey’s Manual of Systematic Bacteriology (BMSB) has been submitted to the publisher, with an expected publication date of late 2011 or early 2012. This multi-volume work describes the systematics, ecology, physiology and other biological properties of prokaryotes. Published by Bergey’s Manual Trust and Springer, it is the most complete and authoritative description of bacterial and archaeal diversity currently published.

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Taxonomic subcommittees and minimal standards for the description of prokaryotes

The preparation of minimal standards for the description of new taxa is one of the tasks of the taxonomic subcommittees working under the auspice of the International Committee on Systematics of Prokaryotes. Minimal standards are intended to provide bacteriologists involved in the taxonomy of prokaryotes a set of essential requirements for the description of new taxa.

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Prokaryotic taxonomy in the sequencing era and the role of MLSA in classification

The initial step in prokaryote species and genera descriptions is now largely based on the 16S rRNA gene sequencing approach followed often by a very restricted additional phenotypic characterisation of the representatives of the potential novel taxa. Despite the advantages of the sequence-based approaches, there appears to be a tendency to classify new species on the basis of comparative sequence analyses of 16S rRNA gene sequences and other gene sequence data (multilocus sequence analyses, MLSA), contrary to the indications of other data. How...

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Capturing and taming Earth’s wild microbes

Among the organisms of the biosphere, the diversity of the Bacteria and Archaea is the most poorly understood. Our lack of knowledge about microbial diversity is important because the majority of these organisms still remain undescribed and unclassified and the roles they perform in their environments, their geochemical activities and their biotechnological potential still need to be ascertained. For these reasons, this rich, unknown diversity comprises an enormous untapped resource for science and society. Only recently have microbiologists be...

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Microbial diversity beyond E. coli: new microbial worlds, new concepts in biology

Microbial diversity explores the universe of microorganisms beyond classical models such as Escherichia coli, influenza virus, or Saccharomyces cerevisiae. Exploring such new microbial worlds is essential for a microbiology which needs to learn about all the scientific and practical possibilities offered by billions of years of microbial evolution. Here we illustrate some examples of how studying a wide range of microbial diversity can assist microbiology as a fundamental and a practical science.

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Proteomic applications in microbial identification

Proteomics-based approaches have been used in microbial taxonomy for the last several decades. Recent improvements in instruments and software have led to the appearance of mass spectrometric fingerprinting and peptide survey approaches allowing for highly rapid and accurate taxonomic diagnoses suitable for high-throughput laboratories as well as means to deeply analyse entire proteomes.

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How can actinomycete taxonomy and natural product research work together? The Sanofi-Aventis approach

The role of taxonomy in natural product research can be estimated in different ways. As the biological active secondary metabolite is in the focus, different companies have developed their own philosophy, as Sanofi-Aventis has done. Surveying the patent literature and journals for the description of natural products, for example, the Journal of Antibiotics, it is found that most actinomycetes reported to produce biological active compounds are described only to the genus level1 or with an invalid taxonomic name. Many of them belong to novel spe...

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Metagenomics and beyond: new toolboxes for microbial systematics

An extraordinary DNA sequencing revolution has taken place over the past decade, which has seen exciting, yet challenging times for microbial genomics and systematics. Numerous metagenomics and metatranscriptomics projects have provided us with an unprecedented glimpse at the vast biological diversity that exists in minute amounts of samples obtained from environments such as ocean water, soil or human distal gut. One of the key challenges is how we catalogue and classify this vast diversity of microbial life (much of which represents uncultura...

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Bacteriophage taxonomy

Bacteriophages or “phages” are viruses of prokaryotes. At least 5,360 tailed and 179 cubic, filamentous, and pleomorphic bacterial viruses have been examined in the electron microscope since the introduction of negative staining in 1959. Since at least 100 novel bacterial viruses are described every year1, the approximate number of viruses under consideration is over 6,000. Numerically, this makes bacteriophages the largest virus group known. Phages are presently classified in a hierarchical and holistic system with one order and 10 families. O...

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Size does matter – distinguishing bacteriophages by genome length (and ‘breadth’)

Genome size and nucleic acid composition are basic characteristics of bacteriophages (phages). With larger genomes come increases in gene number, greater infection and virion sophistication, higher likelihood of gene acquisition via horizontal gene transfer (HGT), and additional genetic redundancy both within and between genomes (the latter referring to gene duplication and redundancy with host functions, respectively). Larger, that is, tailed phages in fact are among the most recombinogenic organisms on earth, often possessing numerous genes o...

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Virus systematics: relationships and names

The core activity of biological systematists is to devise systems – classifications – representing the relationships of groups of organisms, usually their evolutionary relationships. These classifications, together with the names of the organisms – taxonomies – can then be used by all to communicate about the organisms, their characteristics, identification, evolution, adaptations and so on.

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Impact of DNA data on fungal and yeast taxonomy

The species richness and diversity existing in microorganisms are unparalleled on our planet. In recent years, the use of molecular techniques for the detection and identification of microorganisms, especially through DNA sequencing, has revolutionised the way taxonomists look at the systematics of a species, especially when applying multilocus sequence data and concepts such as the genealogical concordance phylogenetic species recognition (GCPSR) concept1. Particularly problematic topics arising in the fungi are, for example, naming pleomorphi...

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World Federation for Culture Collections: professionals underpinning microbial systematics

The World Federation for Culture Collections (WFCC) is a multidisciplinary commission of the International Union of Biological Sciences (IUBS) and a Federation within the International Union of Microbiological Societies (IUMS). The WFCC is concerned with the collection, authentication, maintenance and distribution of cultures of microorganisms and cultured cells. Its aim is to promote and support the establishment of culture collections and related services, to provide liaison and networking between the collections and their users, to organise ...

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Countermeasure to change resistance in

Success in management depends largely on the manager’s strategic leadership ability, self-discipline, reflexivity, and quality of management training received. Recently, strategic management skills have become a major concern in project management; it has been identified that almost 90% of projects fail to deliver value. This shortfall was further highlighted by a recent survey commissioned by IBM Global Business Services involving over 1,500 change practitioners. This study assessed strategies of business, operations, organisational change and...

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Real-time PCR for laboratory diagnosis of Acanthamoeba keratitis

Acanthamoeba keratitis is a painful vision-threatening disease of the human cornea. It is characterised by severe ocular pain or partial paracentral stromal ring infiltrate, which can be frequently misdiagnosed as herpes simplex virus keratitis. If the infection is not treated promptly, it may progress to ulceration of the cornea, loss of visual acuity, possibly blindness and even require enucleation. Acanthamoeba sp are found commonly in freshwater, tap water, seawater, hot springs and swimming pools. An epidemiologic case study revealed that ...

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