Some of the most significant breakthroughs in the biological sciences this century will emerge from the development of next generation sequencing technologies. The ease of availability of DNA sequence made possible through these new technologies has given researchers opportunities to study organisms in a manner that was not possible with Sanger sequencing. Scientists will, therefore, need to embrace genomics, as well as develop and nurture the human capacity to sequence genomes and utilise the 'tsunami' of data that emerge from genome sequencing. In response to these challenges, we sequenced the genome of Fusarium circinatum, a fungal pathogen of pine that causes pitch canker, a disease of great concern to the South African forestry industry. The sequencing work was conducted in South Africa, making F. circinatum the first eukaryotic organism for which the complete genome has been sequenced locally. Here we report on the process that was followed to sequence, assemble and perform a preliminary characterisation of the genome. Furthermore, details of the computer annotation and manual curation of this genome are presented. The F. circinatum genome was found to be nearly 44 million bases in size, which is similar to that of four other Fusarium genomes that have been sequenced elsewhere. The genome contains just over 15 000 open reading frames, which is less than that of the related species, Fusarium oxysporum, but more than that for Fusarium verticillioides. Amongst the various putative gene clusters identified in F. circinatum, those encoding the secondary metabolites fumosin and fusarin appeared to harbour evidence of gene translocation. It is anticipated that similar comparisons of other loci will provide insights into the genetic basis for pathogenicity of the pitch canker pathogen. Perhaps more importantly, this project has engaged a relatively large group of scientists including students in a significant genome project that is certain to provide a platform for growth in this important area of research in the future.

Nontuberculous mycobacteria (NTM) are ubiquitous and have been isolated from a variety of environmental sources, including water. Various NTM were isolated from biofilms in drinking water distribution systems in two urban and two semiurban areas in South Africa. Most of the isolates belonged to opportunistic pathogenic species of the NTM group, but none belonged to the Mycobacterium avium complex.The genus Mycobacterium comprises both the strictly pathogenic species that are transmitted by human or animal reservoirs only (M. tuberculosis, M. leprae) and the so-called nontuberculous mycobacteria (NTM) (3,13,14). The NTM have generally been associated with soil and water, and while many of them are considered to be nonpathogenic, an increasing number are being reported as opportunistic pathogens (3,5,16). This growing number of atypical pathogenic mycobacteria includes M. abscessus (8), M. chelonae (10), M. fortuitum (16,27), M. gordonae (19), M. mageritense (9), and M. xenopi (5). Several NTM constitute a risk not only to immunosuppressed persons but also to otherwise healthy persons (10). They can cause pulmonary and cutaneous diseases, lymphadenitis, and other infections (14).M. abscessus, M. gilvum, M. gordonae, and M. mageritense have been associated with municipal water supplies (7,9,12). In a recent report, furunculosis, caused by M. mageritense, was also linked to the water supply of a salon where two women received footbaths (9). In another report, cervical lymphadenitis in children below 2 years of age has been linked with mycobacteria in the United States, the United Kingdom, and Australia (21). These infections were linked to the prevalence of M. avium and M. scrofulaceum in water (21). There are also reports that NTM can be present in aerosols, such as at swimming pools and spas, of water that may contain mycobacteria and that individuals exposed to the aerosols for extended periods are more at risk of contracting an infection (6). In the United States alone, over a million workers are exposed to aerosols generated by metal grinding, and exposure to such aerosols can lead to hypersensitivity, pneumonitis, and chronic obstructive pulmonary disease (6, 21).NTM are tolerant to a much wider pH and temperature range than are most other bacterial pathogens detected in municipal water supplies. They are also generally tolerant to chlorine, making them potentially more difficult to eliminate (12, 13). Adding to this is their ability to form biofilms on surfaces in drinking water distribution systems (12, 24). The growth of NTM in biofilms may lead to dissemination into the bulk water, constituting a risk to consumers both by drinking and by inhalation of aerosols though showering and swimming.NTM can form biofilms under low-nutrient conditions, making surfaces of drinking water distribution systems an environment for their growth and possible dissemination (12). The aim of this study was to determine the presence and diversity of NTM in biofilms in drinking water distribution systems by analyzing samples from...

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In this study, surface water was used to evaluate the impact of disinfection processes (chlorination, chloramination, ozonation, UV irradiation and hydrogen peroxide) on biofilm formation in potable water distribution systems. Biofilm formation was obvious, even in the presence of residual disinfectant concentrations (16.5 mgl−1 hydrogen peroxide, 1 mg−1 monochloramine, 0.2 mgl−1 free chlorine) within the first day after disinfection in the laboratory scale unit. The yield in viable count was higher on stainless steel coupons than on cement coupons within the first 8 days. Viable bacteria numbers on cement coupons were similar (±2 log cfu.cm−2) in chlorinated, ozonated and in the control. Biofilm formation was related to the depletion of residual disinfectant concentration. Monochloramine and hydrogen peroxide had a longer residual effect controlling growth of biofilm cells in the system for a longer period before regrowth occurred. Once no residual concentrations could be detected there was no significant difference between the viable bacterial counts on any of the coupons in the various systems.

The genus Dracophyllum Labill. (Ericaceae) has a fragmented distribution in Australasia, but reaches the greatest level of species richness and morphological diversity in New Zealand. We investigated evolutionary processes that contribute to this disparity in species richness by comparing DNA sequences from members of Dracophyllum, its close relatives Richea Labill. and Sphenotoma R. Br. ex Sweet (together constituting tribe Richeeae Crayn & Quinn), along with more distant relatives in the Ericaceae. We created complementary data sets for the chloroplast-encoded genes matK and rbcL. Parsimony, Bayesian, and maximum likelihood analyses were conducted to assess the robustness of our phylogenetic inferences. The results were largely congruent and, when analyzed in combination, provided greater resolution. In our analyses, tribe Richeeae formed a monophyletic group that diverged during the Eocene (at least 33.3 million years ago [Ma]) with a crown radiation during the Early Miocene (at least 16.5 Ma) that resulted in two disjunct lineages. This date corresponds roughly to the onset of aridification in central Australia. The southern Western Australian genus Sphenotoma formed an isolated evolutionary lineage, while Dracophyllum and Richea together formed a second lineage restricted to eastern Australia, Lord Howe Island, New Caledonia, and New Zealand. The relationships of the Tasmanian endemic, D. milliganii Hook. f., remain an enigma. It was ambiguously placed as sister to Sphenotoma or to the Dracophyllum-Richea clade. We recovered two distinct lineages, traditionally recognized as Richea sect. Cystanthe (R. Br.) Benth. and Richea sect. Dracophylloides Benth., which were nested within Dracophyllum. The Lord Howe Island endemic, D. fitzgeraldii F. Muell., emerged as sister to an eastern Australian clade of Dracophyllum. Our evidence suggests that the New Caledonian and New Zealand species of Dracophyllum dispersed from Australia; we document two independent episodes of long-distance dispersal in the Late Miocene to Early Pliocene. Low levels of sequence divergence suggest a rapid and recent species radiation in these two island archipelagos largely within the last three to six million years. This radiation accompanied Pliocene uplift of the New Zealand Southern Alps and episodes of glaciation during the Pleistocene. Because Dracophyllum is paraphyletic and Richea is polyphyletic, the taxonomic circumscription of these genera requires revision.