Emma J Gagen

Emma J Gagen
Queensland Government · Department of Environment and Science

About

57
Publications
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Publications

Publications (57)
Article
Full-text available
The Coorong Lakes, South Australia, are one of the models for unravelling the ‘Dolomite Problem’. Critically, today only a few modern environments remain where large quantities of very high magnesium calcite (Ca0.5Mg0.5CO3) (also described as protodolomite or disordered dolomite) and magnesite (MgCO3) precipitate. Previously conducted laboratory st...
Article
Full-text available
Meteorites that fall to Earth quickly become contaminated with terrestrial microorganisms. These meteorites are out of chemical equilibrium in the environments where they fall, and equilibration promotes formation of low-temperature alteration minerals that can entomb contaminant microorganisms and thus preserve them as microfossils. Given the well...
Article
Full-text available
Asgardarchaeota have been proposed as the closest living relatives to eukaryotes, and a total of 72 metagenome-assembled genomes (MAGs) representing six primary lineages in this archaeal phylum have thus far been described. These organisms are predicted to be fermentative heterotrophs contributing to carbon cycling in sediment ecosystems. Here, we...
Article
Bioremediation of degraded lands using biological soil crusts (i.e., biocrusts; complex association between soil, microorganisms. and extracellular polymeric substances) is an emerging biotechnological strategy to control surface erosion. Here, we examined the use of biocrusts for the stabilisation of iron ore mine waste. Simulating naturally occur...
Article
Biofilms enriched in copper (Cu) and zinc (Zn) have formed at the aqueous-air interface and in subaqueous environments at the abandoned Mount Chalmers volcanic-hosted massive sulphide mine in Queensland, Australia. Remedial activity on site has limited acid mine drainage and associated iron-rich discharges, and surface waters leave the site at pH ∼...
Article
Iron ore mine remediation in Brazil presents a unique challenge, distinct from remediation efforts of other lateritic deposits, as a result of the lack of soil. These unique rupestrian (rock associated) ecosystems, including a suite of naturally rare and endemic plant species, are associated with the ironstone (canga) outcrops that commonly cap iro...
Preprint
Full-text available
Asgardarchaeota have been proposed as the closest living relatives to eukaryotes, and a total of 72 metagenome-assembled genomes (MAGs) representing six primary lineages in this archaeal phylum have thus far been described. These organisms are predicted to be fermentative organoheterotrophs contributing to carbon cycling in sediment ecosystems. Her...
Article
The evolution of iron-rich duricrusts (canga) that cap weathered banded iron formations (BIFs) in the Serra Sul de Carajás, northern Brazil, has been essential to armour these landscapes, allowing for the enrichment and preservation of world class iron ore deposits. Bulk chemical data highlight an incorporation of exogenous materials into secondary...
Article
Full-text available
Rare earth elements are increasingly required for use in modern high-tech components, and primary production is necessary to meet the demand. Reprocessing legacy metallurgical tailings is advantageous, as the material has already been mined, beneficiated, upgraded, and contained in a single accessible location. The Mary Kathleen uranium process tai...
Article
Full-text available
We promoted microbial iron reduction and subsequent iron oxidation, in crushed iron‐rich mine waste at pilot scale (~1 m3). Repeated iron cycling led to the formation of new iron oxide cements cementing grains and aggregating the waste material. The technology has promise for accelerating remediation of iron ore mine sites. Accelerating microbial i...
Article
Significance Successful mine remediation is often the missing link in the circular and sustainable model for metal mining. Here, we provide compelling evidence that promoting the biogeochemical cycling of iron can be used to stabilize and remediate mine surfaces using crushed mine waste products. These microbially stabilized iron-rich crusts provid...
Article
Full-text available
Diverse aerobic bacteria persist by consuming atmospheric hydrogen (H2) using group 1h [NiFe]-hydrogenases. However, other hydrogenase classes are also distributed in aerobes, including the group 2a [NiFe]-hydrogenase. Based on studies focused on Cyanobacteria, the reported physiological role of the group 2a [NiFe]-hydrogenase is to recycle H2 prod...
Article
Full-text available
Robust methods for the characterisation of microbial biosignatures in geological matrices is critical for developing mineralogical biosignatures. Studying microbial fossils is fundamental for our understanding of the role microorganisms have played in elemental cycling in modern and ancient environments on Earth and potentially Mars. Here, we aim t...
Article
Iron-rich duricrusts (canga) that blanket iron ore deposits in tropical regions in Brazil have a complex formation and evolution. The direct role of microorganisms in the biogeochemical cycling of iron and remarkably aluminium, which is critical for the preservation of these duricrusts, is becoming more apparent. In this study we combine nanoscale...
Article
Previous data provides evidence that magnetite-rich rock material can sustain large populations of acidophilic, iron-oxidising bacteria. Here we investigate the role of microbially-mediated oxidation of magnetite in more detail, using a strain of Acidithiobacillus ferrooxidans cultured from weathered, iron-rich rocks at the Salobo iron-ore copper-g...
Preprint
Full-text available
Diverse aerobic bacteria persist by consuming atmospheric hydrogen (H2) using group 1h [NiFe]-hydrogenases. However, other hydrogenase classes are also distributed in aerobes, including the group 2a [NiFe]-hydrogenase. Based on studies focused on Cyanobacteria, the reported physiological role of the group 2a [NiFe]-hydrogenase is to recycle H2 prod...
Article
A diverse array of microorganisms, found within the uppermost lithosphere, can mediate the dissolution and precipitation of minerals and therefore contribute to the formation of laterites. The Salobo iron-oxide copper gold (IOCG) mine in Brazil is an ideal environment to examine the specific interaction between iron-oxidising bacteria and ferrous i...
Article
Goethite-cemented duricrusts, also known as canga, commonly occur as a capping rock protecting underlying iron ore deposits. The processes that govern canga formation are still unclear but include recurrent partial dissolution and recrystallisation of goethite through biogeochemical cycling of iron, hypothesised to be catalysed by plants and bacter...
Article
The advent of microfluidics has revolutionized the way we understand how microorganisms propagate through microporous spaces. Here, we apply this understanding to the study of how endolithic environmental microorganisms colonize the interiors of sterile rock. The substrates used for our study are stony meteorites from the Nullarbor Plain, Australia...
Article
Full-text available
In tropical iron ore regions, biologically mediated reduction of crystalline iron oxides drives ongoing iron cycling that contributes to the stability of surface duricrusts. This represents a biotechnological opportunity with respect to post-mining rehabilitation attempts, requiring re-formation of these duricrusts. However, cultivated dissimilator...
Article
The primary ore at the giant Salobo iron oxide copper-gold (IOCG) deposit in Brazil is dominated by magnetite and Fe-rich silicates, with minor (~1%) disseminated Cu-Fe sulphides and a distinctive absence of pyrite. Supergene Fe-silicate and sulphide oxidation has been mediated by bacteria, commonly within micrometre-scale acidic environments, but...
Article
In this study we investigated the potential effects of promoting bacterial activity on tailings from the Salobo iron-oxide copper‑gold (IOCG)mine, Brazil. In particular we focussed on (1)the potential for mobilising additional Cu and (2)the effects of long-term storage on other metals. Unlike typical sulphide-ore tailings, the pH of the Salobo tail...
Article
Supergene enriched iron ore deposits in Brazil are typically blanketed by goethite-cemented breccias that form a protective duricrust known as canga. Moderately hard, well consolidated, permeable and resistant to erosion and chemical weathering, the canga blanket protects the relatively friable iron ore below. The protective canga horizons in the C...
Article
Full-text available
The surface crust that caps highly weathered banded iron formations (BIFs) supports a unique ecosystem that is a post-mining restoration priority in iron ore areas. Geochemical evidence indicates that biological processes drive the dissolution of iron oxide minerals and contribute to the ongoing evolution of this duricrust. However, limited informa...
Article
Demonstrating the biogenicity of presumptive microfossils in the geological record often requires supporting chemical signatures, including isotopic signatures. Understanding the mechanisms that promote the preservation of microbial biosignatures associated with microfossils is fundamental to unravelling the palaeomicrobiological history of the mat...
Article
As the global population increases, so does the demand for minerals and energy resources. Demand for some of the major global commodities is currently growing at rates of: copper – 1.6% p.a.1; iron ore: 1.4% p.a.2; aluminium – 5% p.a.3; rare earth elements – 7% p.a.4, driven not only by population growth in China, India, and Africa, but also by inc...
Article
In numerous global coal–bearing basins, methane, possessing a biogenic stable isotope composition, is spatially and temporally associated with groundwater recharge. However, beyond groundwater inoculating the subsurface with microorganisms, the biological mechanisms that control the distribution of biogenic methane are poorly understood. In this st...
Article
Unambiguous identification of biosignatures on Mars requires access to well-characterized, long-lasting geochemical standards at the planet’s surface that can be modified by theoretical martian life. Ordinary chondrites, which are ancient meteorites that commonly fall to the surface of Mars and Earth, have well-characterized, narrow ranges in trace...
Article
Full-text available
Finding fresh, sterilized rocks provides ecologists with a clean slate to test ideas about first colonization and the evolution of soils de novo. Lava has been used previously in first colonizer studies due to the sterilizing heat required for its formation. However, fresh lava typically falls upon older volcanic successions of similar chemistry an...
Conference Paper
Full-text available
One hurdle to finding evidence for life beyond Earth is being able to identify its chemical, textural and isotopic fingerprints. This is a challenge in environments that can mask biomarker discovery and/or where geochemical and mineralogical limits are still being established. An ideal solution would be to use standards with known chemical and isot...
Article
Full-text available
The majority of cells in nature probably exist in a stationary-phase-like state, due to nutrient limitation in most environments. Studies on bacteria and yeast reveal morphological and physiological changes throughout the stationary phase, which lead to an increased ability to survive prolonged nutrient limitation. However, there is little informat...
Article
The microbial communities present in two underground coal mines in the Bowen Basin, Queensland, Australia, were investigated to deduce the effect of pumping and mining on subsurface methanogens and methanotrophs. The micro-organisms in pumped water from the actively mined areas, as well as, pre- and post-mining formation waters were analyzed using...
Article
Microbe-catalyzed redistribution of metals in the Earth's crust can produce remarkable, and often economic, metal enrichments. These catalytic processes rely on redox transformations to produce secondary-mineral assemblages. Classic supergene systems relate to copper, where weathering is driven by microbial activity. Roll-front uranium deposits rep...
Article
Molecular information suggests that there is a broad diversity of acetogens in the rumen, distinct from any currently isolated acetogens. We combined molecular analysis with enrichment culture techniques to investigate this diversity further. Methane inhibited, hydrogenotrophic enrichment cultures produced acetate as the dominant end product. Acety...
Article
Full-text available
Methanothermobacter thermautotrophicus strain ΔH is a model hydrogenotrophic methanogen, for which extensive biochemical information, including the complete genome sequence, is available. Nevertheless, at the cell membrane lipid level, little is known about the responses of this archaeon to environmental stimuli. In this study, the lipid compositio...
Article
Greenhouse gas (GHG) emissions from livestock is about 7,516 million metric tons CO2-eq.year-1and has multiple components that include enteric methane emissions, methane and nitrous oxide emissions from manure and carbon dioxide emissions associated with feed production and grazing. An uninterruptedly increasing concentration (155 % more than prein...
Chapter
This 395-paged-book aims to raise awareness among scientists, academics, students, livestock farmers and policy makers of the twin inter-related and inter-dependent complex mechanisms of livestock rearing and climate change. The contents are divided into sections: one on livestock production, one on climate change and one on enteric methane amelior...
Article
Full-text available
Background Forestomach fermentation in Australian marsupials such as wallabies and kangaroos, though analogous to rumen fermentation, results in lower methane emissions. Insights into hydrogenotrophy in these systems could help in devising strategies to reduce ruminal methanogenesis. Reductive acetogenesis may be a significant hydrogen sink in thes...
Article
Full-text available
The characteristic glycerol dibiphytanyl glycerol tetraether membrane lipids (GDGTs) of marine ammonia-oxidizing archaea (AOA) are widely used as biomarkers for studying their occurrence and distribution in marine environments and for reconstructing past sea surface temperatures using the TEX86 index. Despite an increasing use of GDGT biomarkers in...
Article
Full-text available
We observed significant changes in the elemental and intact polar lipid (IPL) composition of the archaeon Thermococcus kodakarensis (KOD1) in response to growth stage and phosphorus supply. Reducing the amount of organic supplements and phosphate in growth media resulted in significant decreases in cell size and cellular quotas of carbon (C), nitro...
Data
We observed significant changes in the elemental and intact polar lipid (IPL) composition of the archaeon Thermococcus kodakarensis (KOD1) in response to growth stage and phosphorus supply. Reducing the amount of organic supplements and phosphate in growth media resulted in significant decreases in cell size and cellular quotas of carbon (C), nitro...
Article
Full-text available
The uncultured miscellaneous crenarchaeotic group (MCG) archaea comprise one of the most abundant microbial groups in the Earth's subsurface environment. However, very little information is available regarding the lifestyle, physiology, and factors controlling the distribution of members of this group. We established a novel method using both culti...
Article
Full-text available
Reductive acetogenesis is not competitive with methanogenesis in adult ruminants, whereas acetogenic bacteria are the dominant hydrogenotrophs in the early rumen microbiota. The ecology of hydrogenotrophs in the developing rumen was investigated using young lambs, raised in sterile isolators, and conventional adult sheep. Two lambs were born natura...
Article
Full-text available
Reductive acetogenesis via the acetyl coenzyme A (acetyl-CoA) pathway is an alternative hydrogen sink to methanogenesis in the rumen. Functional gene-based analysis is the ideal approach for investigating organisms capable of this metabolism (acetogens). However, existing tools targeting the formyltetrahydrofolate synthetase gene (fhs) are compromi...
Article
Full-text available
Nucleic acid-based techniques which can be used to characterise complex microbial communities without incubation are now being employed regularly in ruminant nutrition studies. Conventional culture-based methods for enumerating rumen microorganisms (bacteria, archaea, protozoa, and fungi) have been superseded and are now used mainly to obtain pure...
Article
Reductive acetogenesis via the acetyl-CoA pathway is a hydrogenotrophic pathway that has the potential to reduce methanogenesis from ruminant livestock. However our understanding of the organisms capable of this transformation (acetogens) is hindered by a lack of specific molecular tools for this group. In the present thesis, a PCR primer set speci...

Projects

Projects (2)
Project
The goal of this project is to understand how microbes leverage mineral behaviour to scavenge water and nutrients in order to colonise sterile rocks such as meteorites. We are also exploring how mineralogy influences community structure.