The complete genome, comparative and functional analysis of Stenotrophomonas maltophilia reveals an organism heavily shielded by drug resistance determinants

The complete Stenotrophomonas maltophilia genome sequence suggests that it can act as a reservoir of antibiotic resistance determinants

Doing diversity: intercultural understanding in primary and secondary schools

Doing Diversity: Intercultural understanding in primary and secondary schools1 was a three year, multi-method programme of research involving intensive work in 12 diverse profile schools in Melbourne, Victoria, that examined the facilitators and impediments to the intercultural capabilities described in the Victorian and Australian curricula for students and schools

The biogeochemical impact of glacial meltwater from Southwest Greenland

Biogeochemical cycling in high-latitude regions has a disproportionate impact on global nutrient budgets. Here, we introduce a holistic, multi-disciplinary framework for elucidating the influence of glacial meltwaters, shelf currents, and biological production on biogeochemical cycling in high-latitude continental margins, with a focus on the silica cycle. Our findings highlight the impact of significant glacial discharge on nutrient supply to shelf and slope waters, as well as surface and benthic production in these regions, over a range of timescales from days to thousands of years. Whilst biological uptake in fjords and strong diatom activity in coastal waters maintains low dissolved silicon concentrations in surface waters, we find important but spatially heterogeneous additions of particulates into the system, which are transported rapidly away from the shore. We expect the glacially-derived particles – together with biogenic silica tests – to be cycled rapidly through shallow sediments, resulting in a strong benthic flux of dissolved silicon. Entrainment of this benthic silicon into boundary currents may supply an important source of this key nutrient into the Labrador Sea, and is also likely to recirculate back into the deep fjords inshore. This study illustrates how geochemical and oceanographic analyses can be used together to probe further into modern nutrient cycling in this region, as well as the palaeoclimatological approaches to investigating changes in glacial meltwater discharge through time, especially during periods of rapid climatic change in the Late Quaternary

The CISE-LOCEAN sea water isotopic database (1998–2021)

Submitted to journal ESSD (Earth System Science Data)The characteristics of the CISE-LOCEAN sea water isotope data set (δ$^{18}$O, δ2H, later designed as δD) are presented. This data set covers the time period from 1998 to 2021 and currently includes close to 8000 data entries, all with δ$^{18}$O, three quarters of them also with δD, associated with a time and space stamp and usually a salinity measurement. Until 2010, samples were analysed by isotopic ratio mass spectrometry, and since then mostly by cavity ring-down spectroscopy (CRDS). Instrumental uncertainty on individual data in this dataset is usually with a standard deviation as low as 0.03 / 0.15 ‰ for δ$^{18}$O and δD. An additional uncertainty is related to uncertain isotopic composition of the in-house standards that are used to convert daily data into the VSMOW scale. Different comparisons suggest that since 2010 the latter have remained within at most 0.03 / 0.20 ‰ for δ$^{18}$O and δD. Therefore, combining the two suggests a standard deviation of at most 0.05 / 0.25 ‰ for δ$^{18}$O / δD. Finally, for some samples, we find that there has been evaporation during collection and storage, requiring adjustment of the isotopic data produced by CRDS, based on d-excess. This adds an uncertainty on the adjusted data of roughly 0.05 / 0.10 ‰ on δ$^{18}$O and δD. This issue of conservation of samples is certainly a strong source of quality loss for parts of the database, and ‘small’ effects may have remained undetected. The internal consistency of the database can be tested for subsets of the dataset, when time series can be obtained (such as in the southern Indian Ocean or North Atlantic subpolar gyre). These comparisons suggest that the overall uncertainty of the spatially (for a cruise) or temporally (over a year) averaged data is on the order of or less than 0.03 / 0.15 ‰ for δ18O / δD. On the other hand, 17 comparisons with duplicate sea water data analysed in other laboratories or with other data sets in deep regions suggest a larger scatter. When averaging the 17 comparisons done for δ18O, we find a difference close to the adjustment applied at LOCEAN to convert salty water data from the activity to the concentration scale. Such a difference is expected, but the scatter found suggests that care is needed when merging datasets from different laboratories. Examples of time series in the surface North Atlantic subpolar gyre illustrate the temporal changes in water isotope composition that can be detected with a carefully validated dataset

The CISE-LOCEAN seawater isotopic database (1998–2021)

The characteristics of the CISE-LOCEAN seawater isotope dataset (δ18O, δ2H, referred to as δD) are presented (https://doi.org/10.17882/71186; Waterisotopes-CISE-LOCEAN, 2021). This dataset covers the time period from 1998 to 2021 and currently includes close to 8000 data entries, all with δ18O, three-quarters of them also with δD, associated with a date stamp, space stamp, and usually a salinity measurement. Until 2010, samples were analyzed by isotopic ratio mass spectrometry and since then mostly by cavity ring-down spectroscopy (CRDS). Instrumental uncertainty in this dataset is usually as low as 0.03 ‰ for δ18O and 0.15 ‰ for δD. An additional uncertainty is related to the isotopic composition of the in-house standards that are used to convert data to the Vienna Standard Mean Ocean Water (VSMOW) scale. Different comparisons suggest that since 2010 the latter have remained within at most 0.03 ‰ for δ18O and 0.20 ‰ for δD. Therefore, combining the two uncertainties suggests a standard deviation of at most 0.05 ‰ for δ18O and 0.25 ‰ for δD. For some samples, we find that there has been evaporation during collection and storage, requiring adjustment of the isotopic data produced by CRDS, based on d-excess (δD − 8×δ18O). This adjustment adds an uncertainty in the respective data of roughly 0.05 ‰ for δ18O and 0.10 ‰ for δD. This issue of conservation of samples is certainly a strong source of quality loss for parts of the database, and “small” effects may have remained undetected. The internal consistency of the database can be tested for subsets of the dataset when time series can be obtained (such as in the southern Indian Ocean or North Atlantic subpolar gyre). These comparisons suggest that the overall uncertainty of the spatially (for a cruise) or temporally (over a year) averaged data is less than 0.03 ‰ for δ18O and 0.15 ‰ for δD. However, 18 comparisons with duplicate seawater data analyzed in other laboratories or with other datasets in the intermediate and deep ocean suggest a larger scatter. When averaging the 18 comparisons done for δ18O, we find a difference of 0.082 ‰ with a standard error of 0.016 ‰. Such an average difference is expected due to the adjustments applied at LOCEAN to saline water data produced either by CRDS or isotope ratio mass spectrometry (IRMS), but the scatter found suggests that care is needed when merging datasets from different laboratories. Examples of time series in the surface North Atlantic subpolar gyre illustrate the temporal changes in water isotope composition that can be detected with a carefully validated dataset

Insights from the complete genome sequence of Mycobacterium marinum on the evolution of Mycobacterium tuberculosis

Mycobacterium marinum, a ubiquitous pathogen of fish and amphibia, is a near relative of Mycobacterium tuberculosis, the etiologic agent of tuberculosis in humans. The genome of the M strain of M. marinum comprises a 6,636,827-bp circular chromosome with 5424 CDS, 10 prophages, and a 23-kb mercury-resistance plasmid. Prominent features are the very large number of genes (57) encoding polyketide synthases (PKSs) and nonribosomal peptide synthases (NRPSs) and the most extensive repertoire yet reported of the mycobacteria-restricted PE and PPE proteins, and related-ESX secretion systems. Some of the NRPS genes comprise a novel family and seem to have been acquired horizontally. M. marinum is used widely as a model organism to study M. tuberculosis pathogenesis, and genome comparisons confirmed the close genetic relationship between these two species, as they share 3000 orthologs with an average amino acid identity of 85%. Comparisons with the more distantly related Mycobacterium avium subspecies paratuberculosis and Mycobacterium smegmatis reveal how an ancestral generalist mycobacterium evolved into M. tuberculosis and M. marinum. M. tuberculosis has undergone genome downsizing and extensive lateral gene transfer to become a specialized pathogen of humans and other primates without retaining an environmental niche. M. marinum has maintained a large genome so as to retain the capacity for environmental survival while becoming a broad host range pathogen that produces disease strikingly similar to M. tuberculosis. The work described herein provides a foundation for using M. marinum to better understand the determinants of pathogenesis of tuberculosis