ORCID Profile
0000-0002-1213-1257
Current Organisation
University of Tasmania
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Research Topics
In Research Link Australia (RLA), "Research Topics" refer to ANZSRC FOR and SEO codes. These topics are either sourced from ANZSRC FOR and SEO codes listed in researchers' related grants or generated by a large language model (LLM) based on their publications.
Top 5 Research Topics
ANZSRC Field of Research (FoR)
Ecological Impacts of Climate Change | Biological Oceanography | Population, Ecological and Evolutionary Genetics | Oceanography
ANZSRC Socio-Economic Objective (SEO)
Effects of Climate Change and Variability on Antarctic and Sub-Antarctic Environments (excl. Social Impacts) | Antarctic and Sub-Antarctic Flora, Fauna and Biodiversity | Ecosystem Assessment and Management of Antarctic and Sub-Antarctic Environments |
Related Links
Publications
Site U1534
Publisher: International Ocean Discovery Program
Date: 20-05-2021
From the Surface Ocean to the Seafloor: Linking Modern and Paleo-Genetics at the Sabrina Coast, East Antarctica (IN2017_V01)
Publisher: American Geophysical Union (AGU)
Date: 04-2023
DOI: 10.1029/2022JG007252
Abstract: With ongoing climate change, research into the biological changes occurring in particularly vulnerable ecosystems, such as Antarctica, is critical. The Totten Glacier region, Sabrina Coast, is currently experiencing some of the highest rates of thinning across all East Antarctica. An assessment of the microscopic organisms supporting the ecosystem of the marginal sea‐ice zone over the continental rise is important, yet there is a lack of knowledge about the ersity and distribution of these organisms throughout the water column, and their occurrence and/or preservation in the underlying sediments. Here, we provide a taxonomic overview of the modern and ancient marine bacterial and eukaryotic communities of the Totten Glacier region, using a combination of 16S and 18S rRNA licon sequencing (modern DNA) and shotgun metagenomics (sedimentary ancient DNA, sed aDNA). Our data show considerable differences between eukaryote and bacterial signals in the water column versus the sediments. Proteobacteria and diatoms dominate the bacterial and eukaryote composition in the upper water column, while diatoms, dinoflagellates, and haptophytes notably decrease in relative abundance with increasing water depth. Little diatom sed aDNA is preserved in the sediments, which are instead dominated by Proteobacteria and Retaria. We compare the diatom microfossil and sed aDNA record and link the weak preservation of diatom sed aDNA to DNA degradation while sinking through the water column to the seafloor. This study provides the first assessment of DNA transfer from ocean waters to sediments and an overview of the microscopic communities occurring in the climatically important Totten Glacier region.
Site U1537
Publisher: International Ocean Discovery Program
Date: 20-05-2021
Episodes of Early Pleistocene West Antarctic Ice Sheet Retreat Recorded by Iceberg Alley Sediments
Publisher: American Geophysical Union (AGU)
Date: 07-2022
DOI: 10.1029/2022PA004433
Abstract: Ice loss in the Southern Hemisphere has been greatest over the past 30 years in West Antarctica. The high sensitivity of this region to climate change has motivated geologists to examine marine sedimentary records for evidence of past episodes of West Antarctic Ice Sheet (WAIS) instability. Sediments accumulating in the Scotia Sea are useful to examine for this purpose because they receive iceberg‐rafted debris (IBRD) sourced from the Pacific‐ and Atlantic‐facing sectors of West Antarctica. Here we report on the sedimentology and provenance of the oldest of three cm‐scale coarse‐grained layers recovered from this sea at International Ocean Discovery Program Site U1538. These layers are preserved in opal‐rich sediments deposited ∼1.2 Ma during a relatively warm regional climate. Our microCT‐based analysis of the layer's in‐situ fabric confirms its ice‐rafted origin. We further infer that it is the product of an intense but short‐lived episode of IBRD deposition. Based on the petrography of its sand fraction and the Phanerozoic 40 Ar/ 39 Ar ages of hornblende and mica it contains, we conclude that the IBRD it contains was likely sourced from the Weddell Sea and/or Amundsen Sea embayment(s) of West Antarctica. We attribute the high concentrations of IBRD in these layers to “dirty” icebergs calved from the WAIS following its retreat inland from its modern grounding line. These layers also sit at the top of a ∼366‐m thick Pliocene and early Pleistocene sequence that is much more dropstone‐rich than its overlying sediments. We speculate this fact may reflect that WAIS mass‐balance was highly dynamic during the ∼41‐kyr (inter)glacial world.
Detection of fish sedimentary DNA in aquatic systems: A review of methodological challenges and future opportunities
Publisher: Wiley
Date: 28-08-2023
DOI: 10.1002/EDN3.467
Abstract: Environmental DNA studies have proliferated over the last decade, with promising data describing the ersity of organisms inhabiting aquatic and terrestrial ecosystems. The recovery of DNA present in the sediment of aquatic systems (sedDNA) has provided short‐ and long‐term data on a wide range of biological groups (e.g., photosynthetic organisms, zooplankton species) and has advanced our understanding of how environmental changes have affected aquatic communities. However, substantial challenges remain for recovering the genetic material of macro‐organisms (e.g., fish) from sediments, preventing complete reconstructions of past aquatic ecosystems, and limiting our understanding of historic, higher trophic level interactions. In this review, we outline the biotic and abiotic factors affecting the production, persistence, and transport of fish DNA from the water column to the sediments, and address questions regarding the preservation of fish DNA in sediment. We identify sources of uncertainties around the recovery of fish sedDNA arising during the sedDNA workflow. This includes methodological issues related to experimental design, DNA extraction procedures, and the selected molecular method (quantitative PCR, digital PCR, metabarcoding, metagenomics). By evaluating previous efforts (published and unpublished works) to recover fish sedDNA signals, we provide suggestions for future research and propose troubleshooting workflows for the effective detection and quantification of fish sedDNA. With further research, the use of sedDNA has the potential to be a powerful tool for inferring fish presence over time and reconstructing their population and community dynamics.
Site U1538
Publisher: International Ocean Discovery Program
Date: 20-05-2021
Ancient marine sediment DNA reveals diatom transition in Antarctica
Publisher: Springer Science and Business Media LLC
Date: 02-10-2022
DOI: 10.1038/S41467-022-33494-4
Abstract: Antarctica is one of the most vulnerable regions to climate change on Earth and studying the past and present responses of this polar marine ecosystem to environmental change is a matter of urgency. Sedimentary ancient DNA ( sed aDNA) analysis can provide such insights into past ecosystem-wide changes. Here we present authenticated (through extensive contamination control and sed aDNA damage analysis) metagenomic marine eukaryote sed aDNA from the Scotia Sea region acquired during IODP Expedition 382. We also provide a marine eukaryote sed aDNA record of ~1 Mio. years and diatom and chlorophyte sed aDNA dating back to ~540 ka (using taxonomic marker genes SSU, LSU, psbO ). We find evidence of warm phases being associated with high relative diatom abundance, and a marked transition from diatoms comprising % of all eukaryotes prior to ~14.5 ka, to ~50% after this time, i.e., following Meltwater Pulse 1A, alongside a composition change from sea-ice to open-ocean species. Our study demonstrates that sed aDNA tools can be expanded to hundreds of thousands of years, opening the pathway to the study of ecosystem-wide marine shifts and paleo-productivity phases throughout multiple glacial-interglacial cycles.
Site U1535
Publisher: International Ocean Discovery Program
Date: 20-05-2021
An Outlook for the Acquisition of Marine Sedimentary Ancient DNA (sedaDNA) From North Atlantic Ocean Archive Material
Publisher: American Geophysical Union (AGU)
Date: 05-2022
DOI: 10.1029/2021PA004372
Abstract: Studies incorporating sedimentary ancient DNA ( sed aDNA) analyses to investigate paleo‐environments have increased considerably over the last few years, and the possibility of utilizing archived sediment cores from previous field c aigns could unlock an immense resource of s ling material for such paleo‐investigations. However, sed aDNA research is at a high risk of contamination by modern environmental DNA, as sub‐optimal sediment storage conditions may allow for contaminants (e.g., fungi) to grow and become dominant over preserved sed aDNA in the s le. Here, we test the feasibility of sed aDNA analysis applied to archive sediment material from five sites in the North Atlantic, collected between 1994 and 2013. We analyzed two s les (one younger and one older) per site using a metagenomic shotgun approach and were able to recover eukaryotic sed aDNA from all s les. We characterized the authenticity of each s le through sed aDNA fragment size and damage analyses, which allowed us to disentangle sed aDNA and contaminant DNA. Although we determined that contaminant sequences originated mainly from Ascomycota (fungi), most s les were dominated by Emiliania huxleyi , a haptophyte species that commonly blooms in the study region. We attribute the presence of contaminants to non‐ideal s ling and s le storage conditions of the investigated s les. Therefore, while we demonstrate that sed aDNA analysis of archival North Atlantic seafloor sediment s les are generally achievable, we stress the importance of best‐practice ship‐board s ling techniques and storage conditions to minimize contamination. We highly recommend the application of robust bioinformatic tools that help distinguish ancient genetic signals from modern contaminants, especially when working with archive material.
Latitudinal Variance in the Drivers and Pacing of Warmth During Mid‐Pleistocene MIS 31 in the Antarctic Zone of the Southern Ocean
Publisher: American Geophysical Union (AGU)
Date: 08-2022
DOI: 10.1029/2021PA004394
Abstract: Early Pleistocene Marine Isotope Stage (MIS)‐31 (1.081–1.062 Ma) is a unique interval of extreme global warming, including evidence of a West Antarctic Ice Sheet (WAIS) collapse. Here we present a new 1,000‐year resolution, spanning 1.110–1.030 Ma, diatom‐based reconstruction of primary productivity, relative sea surface temperature changes, sea‐ice proximity/open ocean conditions and diatom species absolute abundances during MIS‐31, from the Scotia Sea (59°S) using deep‐sea sediments collected during International Ocean Discovery Program (IODP) Expedition 382. The lower Jaramillo magnetic reversal (base of C1r.1n, 1.071 Ma) provides a robust and independent time‐stratigraphic marker to correlate records from other drill cores in the Antarctic Zone of the Southern Ocean (AZSO). An increase in open ocean species Fragilariopsis kerguelensis in early MIS‐31 at 53°S (Ocean Drilling Program Site 1,094) correlates with increased obliquity forcing, whereas at 59°S (IODP Site U1537 this study) three progressively increasing, successive peaks in the relative abundance of F. kerguelensis correlate with Southern Hemisphere‐phased precession pacing. These observations reveal a complex pattern of ocean temperature change and sustained sea surface temperature increase lasting longer than a precession cycle within the Atlantic sector of the AZSO. Timing of an inferred WAIS collapse is consistent with delayed warmth (possibly driven by sea‐ice dynamics) in the southern AZSO, supporting models that indicate WAIS sensitivity to local sub‐ice shelf melting. Anthropogenically enhanced impingement of relatively warm water beneath the ice shelves today highlights the importance of understanding dynamic responses of the WAIS during MIS‐31, a warmer than Holocene interglacial.
Environmental paleomicrobiology: using DNA preserved in aquatic sediments to its full potential.
Publisher: Wiley
Date: 07-02-2022
Abstract: In-depth knowledge about spatial and temporal variation in microbial ersity and function is needed for a better understanding of ecological and evolutionary responses to global change. In particular, the study of microbial ancient DNA preserved in sediment archives from lakes and oceans can help us to evaluate the responses of aquatic microbes in the past and make predictions about future bio ersity change in those ecosystems. Recent advances in molecular genetic methods applied to the analysis of historically deposited DNA in sediments have not only allowed the taxonomic identification of past aquatic microbial communities but also enabled tracing their evolution and adaptation to episodic disturbances and gradual environmental change. Nevertheless, some challenges remain for scientists to take full advantage of the rapidly developing field of paleo-genetics, including the limited ability to detect rare taxa and reconstruct complete genomes for evolutionary studies. Here, we provide a brief review of some of the recent advances in the field of environmental paleomicrobiology and discuss remaining challenges related to the application of molecular genetic methods to study microbial ersity, ecology, and evolution in sediment archives. We anticipate that, in the near future, environmental paleomicrobiology will shed new light on the processes of microbial genome evolution and microbial ecosystem responses to quaternary environmental changes at an unprecedented level of detail. This information can, for ex le, aid geological reconstructions of biogeochemical cycles and predict ecosystem responses to environmental perturbations, including in the context of human-induced global changes.
An optimized method for the extraction of ancient eukaryote DNA from marine sediments
Publisher: Wiley
Date: 13-05-2020
Expedition 382 methods
Publisher: International Ocean Discovery Program
Date: 20-05-2021
Ancient DNA and microfossils reveal dynamics of three harmful dinoflagellate species off Eastern Tasmania, Australia, over the last 9,000 years
Publisher: Cold Spring Harbor Laboratory
Date: 18-02-2021
DOI: 10.1101/2021.02.18.431790
Abstract: Harmful algal blooms (HABs) have significantly impacted the seafood industry along the Tasmanian east coast over the past three decades, and are expected to change in frequency and magnitude due to climate change induced changing oceanographic conditions. To investigate the long-term history of regional HABs, a combination of palynological and sedimentary ancient DNA ( sed aDNA) analyses was applied to marine sediment cores from inshore (up to 145 years old) and offshore (up to ~9,000 years) sites at Maria Island, southeast Tasmania. Analyses focused Paralytic Shellfish Toxin (PST) producing dinoflagellates Alexandrium catenella and Gymnodinium catenatum , and the red-tide dinoflagellate Noctiluca scintillans , which were specifically targeted using a hybridization capture sed aDNA technique. Identification of primulin-stained A. catenella cysts throughout the inshore sediment core, together with sed aDNA evidence of a bloom-phase of Alexandrium ~15 years ago, indicates recent stimulation of a cryptic endemic population. Morphologically similar but unstained Alexandrium cysts were observed throughout the offshore core, with sed aDNA confirming the presence of A. catenella from ~8,300 years ago to present. Gymnodinium catenatum cysts were detected only in inshore surface sediments from 30 years ago to present, supporting previous evidence of a 1970s introduction via shipping ballast water. sed aDNA confirmed the presence of G. catenatum -related sequences in the inshore and offshore cores, however, unambiguous species identification could not be achieved due to limited reference sequence coverage of Gymnodinium . Our hybridization capture sed aDNA data also confirmed the historically recent dispersal of the non-fossilizing dinoflagellate Noctiluca scintillans , detected inshore from ~30 years ago, matching first observations of this species in Tasmanian waters in 1994. At the offshore site, N. scintillans sed aDNA was detected only in surface sediments, confirming a recent climate-driven range expansion this species. This study provides new insights into the distribution and abundance of three HAB species in the Tasmanian region, including clues to past bloom phases. Further research into paleo-environmental conditions and paleo-community structure are required to identify the factors driving bloom phases through time and predict plankton community responses under different future climate scenarios. Dinocyst and sed aDNA analyses were applied to marine sediments off Tasmania Alexandrium catenella has been endemic to Australia for at least ~9,000 years Recent A. catenella blooms are likely induced by climate and oceanographic change Gymnodinium catenatum cysts in recent (~30y) sediments confirm a 1970s introduction Noctiluca scintillans sed aDNAin recent (~30y) sediments matches a 1994 introduction
Variability in diatom and silicoflagellate assemblages during mid-Pliocene glacial-interglacial cycles determined in Hole U1361A of IODP Expedition 318, Antarctic Wilkes Land Margin
Publisher: Elsevier BV
Date: 03-2018
First observations of living sea-ice diatom agglomeration to tintinnid loricae in East Antarctica
Publisher: Oxford University Press (OUP)
Date: 13-07-2017
Hybridisation capture allows DNA damage analysis of ancient marine eukaryotes
Publisher: Cold Spring Harbor Laboratory
Date: 25-09-2020
DOI: 10.1101/2020.09.25.310920
Abstract: Marine sedimentary ancient DNA ( sed aDNA) is increasingly used to study past ocean ecosystems, however, studies have been severely limited by the very low amounts of DNA preserved in the subseafloor, and the lack of bioinformatic tools to authenticate sed aDNA in metagenomic data. We applied a hybridisation capture ‘baits’ technique to target marine eukaryote sed aDNA (specifically, phytoplankton, ‘Phytobaits1’ and harmful algal bloom taxa, ‘HABbaits1’), which resulted in up to 4- and 9-fold increases, respectively, in the relative abundance of eukaryotes compared to shotgun sequencing. We further used the new bioinformatic tool ‘HOPS’ to authenticate the sed aDNA component, establishing a new proxy to assess sed aDNA authenticity, the Ancient: Default (A:D) sequences ratio, here positively correlated with subseafloor depth, and generated the first-ever DNA damage profiles of a key phytoplankton, the ubiquitous coccolithophore Emiliania huxleyi. Our study opens new options for the detailed investigation of marine eukaryotes and their evolution over geological timescales.
Expedition 382 summary
Publisher: International Ocean Discovery Program
Date: 20-05-2021
Site U1536
Publisher: International Ocean Discovery Program
Date: 20-05-2021
Antiphased dust deposition and productivity in the Antarctic Zone over 1.5 million years
Publisher: Springer Science and Business Media LLC
Date: 19-04-2022
DOI: 10.1038/S41467-022-29642-5
Abstract: The Southern Ocean paleoceanography provides key insights into how iron fertilization and oceanic productivity developed through Pleistocene ice-ages and their role in influencing the carbon cycle. We report a high-resolution record of dust deposition and ocean productivity for the Antarctic Zone, close to the main dust source, Patagonia. Our deep-ocean records cover the last 1.5 Ma, thus doubling that from Antarctic ice-cores. We find a 5 to 15-fold increase in dust deposition during glacials and a 2 to 5-fold increase in biogenic silica deposition, reflecting higher ocean productivity during interglacials. This antiphasing persisted throughout the last 25 glacial cycles. Dust deposition became more pronounced across the Mid-Pleistocene Transition (MPT) in the Southern Hemisphere, with an abrupt shift suggesting more severe glaciations since ~0.9 Ma. Productivity was intermediate pre-MPT, lowest during the MPT and highest since 0.4 Ma. Generally, glacials experienced extended sea-ice cover, reduced bottom-water export and Weddell Gyre dynamics, which helped lower atmospheric CO 2 levels.
Paleo-diatom composition from Santa Barbara Basin deep-sea sediments: a comparison of 18S-V9 and diat-rbcL metabarcoding vs shotgun metagenomics
Publisher: Springer Science and Business Media LLC
Date: 09-11-2021
DOI: 10.1038/S43705-021-00070-8
Abstract: Sedimentary ancient DNA ( sed aDNA) analyses are increasingly used to reconstruct marine ecosystems. The majority of marine sed aDNA studies use a metabarcoding approach (extraction and analysis of specific DNA fragments of a defined length), targeting short taxonomic marker genes. Promising ex les are 18S-V9 rRNA (~121–130 base pairs, bp) and diat-rbcL (76 bp), targeting eukaryotes and diatoms, respectively. However, it remains unknown how 18S-V9 and diat-rbcL derived compositional profiles compare to metagenomic shotgun data, the preferred method for ancient DNA analyses as lification biases are minimised. We extracted DNA from five Santa Barbara Basin sediment s les (up to ~11 000 years old) and applied both a metabarcoding ( 18S-V9 rRNA , diat-rbcL ) and a metagenomic shotgun approach to (i) compare eukaryote, especially diatom, composition, and (ii) assess sequence length and database related biases. Eukaryote composition differed considerably between shotgun and metabarcoding data, which was related to differences in read lengths (~112 and ~161 bp, respectively), and over lification of short reads in metabarcoding data. Diatom composition was influenced by reference bias that was exacerbated in metabarcoding data and characterised by increased representation of Chaetoceros , Thalassiosira and Pseudo-nitzschia . Our results are relevant to sed aDNA studies aiming to accurately characterise paleo-ecosystems from either metabarcoding or metagenomic data.
Related Organisations
Related Funding Activities
Discovery Early Career Researcher Award - Grant ID: DE210100929
Start Date: 08-2021
End Date: 08-2024
Amount: $462,948.00
Funder: Australian Research Council
View Funded Activity