ORCID Profile
0000-0002-8927-2066
Current Organisation
University of Queensland
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Microbial Ecology | Microbiology | Genomics | Phylogeny and Comparative Analysis | Bioinformatics | Conservation and Biodiversity
Expanding Knowledge in the Biological Sciences | Flora, Fauna and Biodiversity at Regional or Larger Scales |
Publisher: The Endocrine Society
Date: 22-02-2019
Publisher: American Association for the Advancement of Science (AAAS)
Date: 31-03-2017
Abstract: Oxygen-producing photosynthesis and oxygen-consuming respiration evolved after the ergence of the main lineages of blue-green algae.
Publisher: Springer Science and Business Media LLC
Date: 11-06-2011
DOI: 10.1007/S10126-010-9300-4
Abstract: Cultivation of sponges is being explored to supply biomaterial for the pharmaceutical and cosmetics industries. This study assesses the impact of various cultivation methods on the microbial community within the sponge Rhopaloeides odorabile during: (1) in situ cultivation under natural environmental conditions, (2) ex situ cultivation in small flow-through aquaria and (3) ex situ cultivation in large mesocosm systems. Principal components analysis of denaturing gradient gel electrophoresis profiles indicated a stable microbial community in sponges cultured in situ (grown in the wild) and in sponges cultured ex situ in small flow-through aquaria over 12 weeks. In contrast, a shift in the microbial community was detected in sponges cultivated ex situ in large mesocosm aquaria for 12 months. This shift included (1) a loss of some stable microbial inhabitants, including members of the Poribacteria, Chloroflexi and Acidobacteria and (2) the addition of new microbes not detected in the wild sponges. Many of these acquired bacteria had highest similarity to known sponge-associated microbes, indicating that the sponge may be capable of actively selecting its microbial community. Alternatively, long-term ex situ cultivation may cause a shift in the dominant microbes that facilitates the growth of the more rare species. The microbial community composition varied between sponges cultivated in mesocosm aquaria with different nutrient concentrations and seawater chemistry, suggesting that these variables play a role in structuring the sponge-associated microbes. The high growth and symbiont stability in R. odorabile cultured in situ confirm that this is the preferred method of aquaculture for this species at this time.
Publisher: Cold Spring Harbor Laboratory
Date: 11-08-2023
DOI: 10.1101/2023.08.08.552427
Abstract: Most of life’s ersity and history is microbial but it has left a meagre fossil record, greatly hindering understanding of evolution in deep time. However, the co-evolution of life and the Earth system has left signatures of bacterial metabolism in the geochemical record, most conspicuously the Great Oxidation Event (GOE) ∼2.33 billion years ago (Ga, (Poulton et al. 2021)), in which oxygenic photosynthesis and tectonism (Eguchi, Seales, and Dasgupta 2019) transformed Earth’s biosphere from dominantly anaerobic to aerobic. Here, we combine machine learning and phylogenetic reconciliation to infer ancestral transitions to aerobic lifestyles during bacterial evolution. Linking these transitions to the GOE provides new constraints to infer the timetree of Bacteria. We find that extant bacterial phyla are truly ancient, having radiated in the Archaean and the Proterozoic: the oldest include Bacillota (Firmicutes), which radiated 3.1-3.7 Ga, Cyanobacteria (3.3-3.5 Ga) and Patescibacteria (3-3.5 Ga). We show that most bacterial phyla were ancestrally anaerobic and that most transitions to an aerobic lifestyle post-dated the GOE. Our analyses trace oxygen production and consumption back to Cyanobacteria. From that starting point, horizontal transfer seeded aerobic lifestyles across bacterial ersity over hundreds of millions of years. Our analyses demonstrate that the ersification of aerobes proceeded in two waves corresponding to the GOE and to a second sustained rise in atmospheric O 2 at the dawn of the Palezoic (Krause et al. 2022).
Publisher: Elsevier BV
Date: 08-2019
DOI: 10.1016/J.FREERADBIOMED.2019.03.029
Abstract: For well over a hundred years, members of the bacterial phylum Cyanobacteria have been considered strictly photosynthetic microorganisms, reflected in their classification as "blue-green algae" in the botanical code. Recently, genomes recovered from environmental sequencing surveys representing two major uncultured basal lineages (classes) of Cyanobacteria have been found to completely lack photosynthetic and CO
Publisher: Oxford University Press (OUP)
Date: 05-2014
DOI: 10.1093/GBE/EVU073
Publisher: Wiley
Date: 28-03-2008
DOI: 10.1111/J.1462-2920.2008.01593.X
Abstract: Biotic communities and ecosystem dynamics in terrestrial Antarctica are limited by an array of extreme conditions including low temperatures, moisture and organic matter availability, high salinity, and a paucity of bio ersity to facilitate key ecological processes. Recent studies have discovered that the prokaryotic communities in these extreme systems are highly erse with patchy distributions. Investigating the physical and biological controls over the distribution and activity of microbial bio ersity in Victoria Land is essential to understanding ecological functioning in this region. Currently, little information on the distribution, structure and activity of soil communities anywhere in Victoria Land are available, and their sensitivity to potential climate change remains largely unknown. We investigated soil microbial communities from low- and high-productivity habitats in an isolated Antarctic location to determine how the soil environment impacts microbial community composition and structure. The microbial communities in Luther Vale, Northern Victoria Land were analysed using bacterial 16S rRNA gene clone libraries and were related to soil geochemical parameters and classical morphological analysis of soil metazoan invertebrate communities. A total of 323 16S rRNA gene sequences analysed from four soils spanning a productivity gradient indicated a high ersity (Shannon-Weaver values > 3) of phylotypes within the clone libraries and distinct differences in community structure between the two soil productivity habitats linked to water and nutrient availability. In particular, members of the Deinococcus/Thermus lineage were found exclusively in the drier, low-productivity soils, while Gammaproteobacteria of the genus Xanthomonas were found exclusively in high-productivity soils. However, rarefaction curves indicated that these microbial habitats remain under-s led. Our results add to the recent literature suggesting that there is a higher bio ersity within Antarctic soils than previously expected.
Publisher: Wiley
Date: 03-2009
DOI: 10.1111/J.1462-2920.2009.01859.X
Abstract: Tramway Ridge, located near the summit of Mount Erebus in Antarctica, is probably the most remote geothermal soil habitat on Earth. Steam fumaroles maintain moist, hot soil environments creating extreme local physicochemical differentials. In this study a culture-independent approach combining automated rRNA intergenic spacer analysis (ARISA) and a 16S rRNA gene library was used to characterize soil microbial (Bacterial and Archaeal) ersity along intense physicochemical gradients. Statistical analysis of ARISA data showed a clear delineation between bacterial community structure at sites close to fumaroles and all other sites. Temperature and pH were identified as the primary drivers of this demarcation. A clone library constructed from a high-temperature site led to the identification of 18 novel bacterial operational taxonomic units (OTUs). All 16S rRNA gene sequences were deep branching and distantly (85-93%) related to other environmental clones. Five of the signatures branched with an unknown group between candidate ision OP10 and Chloroflexi. Within this clade, sequence similarity was low, suggesting it contains several yet-to-be described bacterial groups. Five archaeal OTUs were obtained and exhibited high levels of sequence similarity (95-97%) with Crenarchaeota sourced from deep-subsurface environments on two distant continents. The novel bacterial assemblage coupled with the unique archaeal affinities reinvigorates the hypotheses that Tramway Ridge organisms are relics of archaic microbial lineages specifically adapted to survive in this harsh environment and that this site may provide a portal to the deep-subsurface biosphere.
Publisher: Wiley
Date: 11-10-0011
DOI: 10.1111/J.1758-2229.2011.00296.X
Abstract: Marine sponges are critical components of benthic environments however, their sessile habit, requirement to filter large volumes of water and complex symbiotic partnerships make them particularly vulnerable to the effects of global climate change. We assessed the effect of elevated seawater temperature on bacterial communities in larvae of the Great Barrier Reef sponge, Rhopaloeides odorabile. In contrast to the strict thermal threshold of 32°C previously identified in adult R. odorabile, larvae exhibit a markedly higher thermal tolerance, with no adverse health effects detected at temperatures below 36°C. Similarly, larval microbial communities were conserved at temperatures up to 34°C with a highly significant shift occurring after 24 h at 36°C. This shift involved the loss of previously described symbionts (in particular the Nitrospira, Chloroflexi and a Roseobacter lineage) and the appearance of new Gammaproteobacteria not detected at lower temperatures. Here, we demonstrated that sponge larvae maintain highly stable symbioses at seawater temperatures exceeding those that are predicted under current climate change scenarios. In addition, by revealing that the shift in microbial composition occurs in conjunction with necrosis and mortality of larvae at 36°C we have provided additional evidence of the strong link between host health and the stability of symbiont communities.
Publisher: Inter-Research Science Center
Date: 17-04-2009
DOI: 10.3354/MEPS07933
Publisher: Springer Science and Business Media LLC
Date: 14-10-2010
Publisher: Public Library of Science (PLoS)
Date: 16-05-2012
Publisher: PeerJ
Date: 21-05-2015
DOI: 10.7717/PEERJ.968
Publisher: Springer Science and Business Media LLC
Date: 10-01-2013
Publisher: Springer Science and Business Media LLC
Date: 25-06-2013
Publisher: Springer Science and Business Media LLC
Date: 21-08-2019
Publisher: Frontiers Media SA
Date: 2012
Publisher: Wiley
Date: 28-10-2013
Abstract: Microorganisms form symbiotic partnerships with a erse range of marine organisms and can be critical to the health and survival of their hosts. Despite the importance of these relationships, the sensitivity of symbiotic microbes to ocean acidification (OA) is largely unknown and this needs to be redressed to adequately predict marine ecosystem resilience in a changing climate. We adopted a profiling approach to explore the sensitivity of microbes associated with coral reef biofilms and representatives of three ecologically important calcifying invertebrate phyla [corals, foraminifera and crustose coralline algae (CCA)] to OA. The experimental design for this study comprised four pHs consistent with current IPCC predictions for the next few centuries (pHNIST 8.1, 7.9, 7.7, 7.5) these pH CO₂ conditions were produced in flow-through aquaria using CO₂ bubbling. All reduced pH/increased pCO₂ treatments caused clear differences in the microbial communities associated with coral, foraminifera, CCA and reef biofilms over 6 weeks, while no visible signs of host stress were detected over this period. The microbial communities of coral, foraminifera, CCA and biofilms were significantly different between pH 8.1 (pCO₂ = 464 μatm) and pH 7.9 (pCO₂ = 822 μatm), a concentration likely to be exceeded by the end of the present century. This trend continued at lower pHs/higher pCO₂. 16S rRNA gene sequencing revealed variable and species-specific changes in the microbial communities with no microbial taxa consistently present or absent from specific pH treatments. The high sensitivity of coral, foraminifera, CCA and biofilm microbes to OA conditions projected to occur by 2100 is a concern for reef ecosystems and highlights the need for urgent research to assess the implications of microbial shifts for host health and coral reef processes.
Publisher: Springer Science and Business Media LLC
Date: 06-04-2021
DOI: 10.1038/S41396-021-00941-X
Abstract: The classification of life forms into a hierarchical system (taxonomy) and the application of names to this hierarchy (nomenclature) is at a turning point in microbiology. The unprecedented availability of genome sequences means that a taxonomy can be built upon a comprehensive evolutionary framework, a longstanding goal of taxonomists. However, there is resistance to adopting a single framework to preserve taxonomic freedom, and ever increasing numbers of genomes derived from uncultured prokaryotes threaten to overwhelm current nomenclatural practices, which are based on characterised isolates. The challenge ahead then is to reach a consensus on the taxonomic framework and to adapt and scale the existing nomenclatural code, or create a new code, to systematically incorporate uncultured taxa into the chosen framework.
Start Date: 2019
End Date: 2021
Funder: Australian Research Council
View Funded ActivityStart Date: 07-2019
End Date: 12-2023
Amount: $387,103.00
Funder: Australian Research Council
View Funded ActivityStart Date: 02-2021
End Date: 01-2024
Amount: $467,000.00
Funder: Australian Research Council
View Funded Activity