School of Geography, Earth and Atmospheric Sciences - Research Publications
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ItemNo Preview AvailableImpact of Surface Functionalization on the Quantum Coherence of Nitrogen-Vacancy Centers in Nanodiamonds(AMER CHEMICAL SOC, 2018-04-18)Nanoscale quantum probes such as the nitrogen-vacancy (NV) center in diamonds have demonstrated remarkable sensing capabilities over the past decade as control over fabrication and manipulation of these systems has evolved. The biocompatibility and rich surface chemistry of diamonds has added to the utility of these probes but, as the size of these nanoscale systems is reduced, the surface chemistry of diamond begins to impact the quantum properties of the NV center. In this work, we systematically study the effect of the diamond surface chemistry on the quantum coherence of the NV center in nanodiamonds (NDs) 50 nm in size. Our results show that a borane-reduced diamond surface can on average double the spin relaxation time of individual NV centers in nanodiamonds when compared to thermally oxidized surfaces. Using a combination of infrared and X-ray absorption spectroscopy techniques, we correlate the changes in quantum relaxation rates with the conversion of sp2 carbon to C-O and C-H bonds on the diamond surface. These findings implicate double-bonded carbon species as a dominant source of spin noise for near surface NV centers. The link between the surface chemistry and quantum coherence indicates that through tailored engineering of the surface, the quantum properties and magnetic sensitivity of these nanoscale systems may approach that observed in bulk diamond.
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ItemThe Hole in the Ozone: The environmental issue we managed to fix* and why we still need to be sunsmart(University of Melbourne, 2015-12-21)
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ItemAustralia emits mercury at double the global average( 2017-08-17)
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ItemPartitioning of Mg, Sr, Ba and U into a subaqueous calcite speleothem(PERGAMON-ELSEVIER SCIENCE LTD, 2019-11-01)The trace-element geochemistry of speleothems is becoming increasingly used for reconstructing palaeoclimate, with a particular emphasis on elements whose concentrations vary according to hydrological conditions at the cave site (e.g. Mg, Sr, Ba and U). An important step in interpreting trace-element abundances is understanding the underlying processes of their incorporation. This includes quantifying the fractionation between the solution and speleothem carbonate via partition coefficients (where the partitioning (D) of element X (DX) is the molar ratio [X/Ca] in the calcite divided by the molar ratio [X/Ca] in the parent water) and evaluating the degree of spatial variability across time-constant speleothem layers. Previous studies of how these elements are incorporated into speleothems have focused primarily on stalagmites and their source waters in natural cave settings, or have used synthetic solutions under cave-analogue laboratory conditions to produce similar dripstones. However, dripstones are not the only speleothem types capable of yielding useful palaeoclimate information. In this study, we investigate the incorporation of Mg, Sr, Ba and U into a subaqueous calcite speleothem (CD3) growing in a natural cave pool in Italy. Pool-water measurements extending back 15 years reveal a remarkably stable geochemical environment owing to the deep cave setting, enabling the calculation of precise solution [X/Ca]. We determine the trace element variability of ‘modern’ subaqueous calcite from a drill core taken through CD3 to derive DMg, DSr, DBa and DU then compare these with published cave, cave-analogue and seawater-analogue studies. The DMg for CD3 is anomalously high (0.042 ± 0.002) compared to previous estimates at similar temperatures (∼8 °C). The DSr (0.100 ± 0.007) is similar to previously reported values, but data from this study as well as those from Tremaine and Froelich (2013) and Day and Henderson (2013) suggest that [Na/Sr] might play an important role in Sr incorporation through the potential for Na to outcompete Sr for calcite non-lattice sites. DBa in CD3 (0.086 ± 0.008) is similar to values derived by Day and Henderson (2013) under cave-analogue conditions, whilst DU (0.013 ± 0.002) is almost an order of magnitude lower, possibly due to the unusually slow speleothem growth rates (<1 μm a−1), which could expose the crystal surfaces to leaching of uranyl carbonate. Finally, laser-ablation ICP-MS analysis of the upper 7 μm of CD3, regarded as ‘modern’ for the purposes of this study, reveals considerable heterogeneity, particularly for Sr, Ba and U, which is potentially indicative of compositional zoning. This reinforces the need to conduct 2D mapping and/or multiple laser passes to capture the range of time-equivalent elemental variations prior to palaeoclimate interpretation.
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ItemCRISPR immunity drives rapid phage genome evolution in Streptococcus thermophilus.(American Society for Microbiology, 2015-04-21)UNLABELLED: Many bacteria rely on CRISPR-Cas systems to provide adaptive immunity against phages, predation by which can shape the ecology and functioning of microbial communities. To characterize the impact of CRISPR immunization on phage genome evolution, we performed long-term bacterium-phage (Streptococcus thermophilus-phage 2972) coevolution experiments. We found that in this species, CRISPR immunity drives fixation of single nucleotide polymorphisms that accumulate exclusively in phage genome regions targeted by CRISPR. Mutation rates in phage genomes highly exceed those of the host. The presence of multiple phages increased phage persistence by enabling recombination-based formation of chimeric phage genomes in which sequences heavily targeted by CRISPR were replaced. Collectively, our results establish CRISPR-Cas adaptive immunity as a key driver of phage genome evolution under the conditions studied and highlight the importance of multiple coexisting phages for persistence in natural systems. IMPORTANCE: Phages remain an enigmatic part of the biosphere. As predators, they challenge the survival of host bacteria and archaea and set off an "arms race" involving host immunization countered by phage mutation. The CRISPR-Cas system is adaptive: by capturing fragments of a phage genome upon exposure, the host is positioned to counteract future infections. To investigate this process, we initiated massive deep-sequencing experiments with a host and infective phage and tracked the coevolution of both populations over hundreds of days. In the present study, we found that CRISPR immunity drives the accumulation of phage genome rearrangements (which enable longer phage survival) and escape mutations, establishing CRISPR as one of the fundamental drivers of phage evolution.
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ItemEcological distribution and population physiology defined by proteomics in a natural microbial community(WILEY, 2010-06)An important challenge in microbial ecology is developing methods that simultaneously examine the physiology of organisms at the molecular level and their ecosystem level interactions in complex natural systems. We integrated extensive proteomic, geochemical, and biological information from 28 microbial communities collected from an acid mine drainage environment and representing a range of biofilm development stages and geochemical conditions to evaluate how the physiologies of the dominant and less abundant organisms change along environmental gradients. The initial colonist dominates across all environments, but its proteome changes between two stable states as communities diversify, implying that interspecies interactions affect this organism's metabolism. Its overall physiology is robust to abiotic environmental factors, but strong correlations exist between these factors and certain subsets of proteins, possibly accounting for its wide environmental distribution. Lower abundance populations are patchier in their distribution, and proteomic data indicate that their environmental niches may be constrained by specific sets of abiotic environmental factors. This research establishes an effective strategy to investigate ecological relationships between microbial physiology and the environment for whole communities in situ.
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ItemMetabolome-proteome differentiation coupled to microbial divergence.(American Society for Microbiology, 2010-10-26)Tandem high-throughput proteomics and metabolomics were employed to functionally characterize natural microbial biofilm communities. Distinct molecular signatures exist for each analyzed sample. Deconvolution of the high-resolution molecular data demonstrates that identified proteins and detected metabolites exhibit organism-specific correlation patterns. These patterns are reflective of the functional differentiation of two bacterial species that share the same genus and that co-occur in the sampled microbial communities. Our analyses indicate that the two species have similar niche breadths and are not in strong competition with one another.
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ItemMinimum information about a single amplified genome (MISAG) and a metagenome-assembled genome (MIMAG) of bacteria and archaea(NATURE PUBLISHING GROUP, 2017-08)We present two standards developed by the Genomic Standards Consortium (GSC) for reporting bacterial and archaeal genome sequences. Both are extensions of the Minimum Information about Any (x) Sequence (MIxS). The standards are the Minimum Information about a Single Amplified Genome (MISAG) and the Minimum Information about a Metagenome-Assembled Genome (MIMAG), including, but not limited to, assembly quality, and estimates of genome completeness and contamination. These standards can be used in combination with other GSC checklists, including the Minimum Information about a Genome Sequence (MIGS), Minimum Information about a Metagenomic Sequence (MIMS), and Minimum Information about a Marker Gene Sequence (MIMARKS). Community-wide adoption of MISAG and MIMAG will facilitate more robust comparative genomic analyses of bacterial and archaeal diversity.
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ItemA novel three-unit tRNA splicing endonuclease found in ultrasmall Archaea possesses broad substrate specificity(OXFORD UNIV PRESS, 2011-12)tRNA splicing endonucleases, essential enzymes found in Archaea and Eukaryotes, are involved in the processing of pre-tRNA molecules. In Archaea, three types of splicing endonuclease [homotetrameric: α(4), homodimeric: α(2), and heterotetrameric: (αβ)(2)] have been identified, each representing different substrate specificity during the tRNA intron cleavage. Here, we discovered a fourth type of archaeal tRNA splicing endonuclease (ε(2)) in the genome of the acidophilic archaeon Candidatus Micrarchaeum acidiphilum, referred to as ARMAN-2 and its closely related species, ARMAN-1. The enzyme consists of two duplicated catalytic units and one structural unit encoded on a single gene, representing a novel three-unit architecture. Homodimeric formation was confirmed by cross-linking assay, and site-directed mutagenesis determined that the conserved L10-pocket interaction between catalytic and structural unit is necessary for the assembly. A tRNA splicing assay reveal that ε(2) endonuclease cleaves both canonical and non-canonical bulge-helix-bulge motifs, similar to that of (αβ)(2) endonuclease. Unlike other ARMAN and Euryarchaeota, tRNAs found in ARMAN-2 are highly disrupted by introns at various positions, which again resemble the properties of archaeal species with (αβ)(2) endonuclease. Thus, the discovery of ε(2) endonuclease in an archaeon deeply branched within Euryarchaeota represents a new example of the coevolution of tRNA and their processing enzymes.