ORCID Profile
0000-0002-5997-522X
Current Organisation
University of Glasgow
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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)
Microbial Ecology | Surface Processes | Geology | Geochemistry | Archaeological Science | Inorganic Geochemistry | Geochronology | Environmental Biotechnology | Biodiscovery | Geochemistry not elsewhere classified | Genetics | Organic Geochemistry | Infectious Agents | Genomics | Hydrometallurgy | Bioremediation |
ANZSRC Socio-Economic Objective (SEO)
Expanding Knowledge in the Biological Sciences | Expanding Knowledge in the Earth Sciences | Expanding Knowledge in History and Archaeology | Ecosystem Adaptation to Climate Change | Climate Change Mitigation Strategies | Climate Change Adaptation Measures | Management of Water Consumption by Mineral Resource Activities | Soils not elsewhere classified | Respiratory System and Diseases (incl. Asthma) | Marine Oceanic Processes (excl. climate related) | Biofuel (Biomass) Energy | Physical and Chemical Conditions of Water in Coastal and Estuarine Environments | Rehabilitation of Degraded Coastal and Estuarine Environments | Mining and Extraction of Titanium Minerals, Zircon, and Rare Earth Metal Ores (e.g. Monazite) | Mining Land and Water Management | Infectious Diseases
Related Links
Publications
Thiocyanate biodegradation: Harnessing microbial metabolism for mine remediation
Publisher: CSIRO Publishing
Date: 2018
DOI: 10.1071/MA18047
Abstract: Thiocyanate (SCN–) forms in the reaction between cyanide (CN–) and reduced sulfur species, e.g. in gold ore processing and coal-coking wastewater streams, where it is present at millimolar (mM) concentrations1. Thiocyanate is also present naturally at nM to µM concentrations in uncontaminated aquatic environments2. Although less toxic than its precursor CN–, SCN– can harm plants and animals at higher concentrations3, and thus needs to be removed from wastewater streams prior to disposal or reuse. Fortunately, SCN– can be biodegraded by microorganisms as a supply of reduced sulfur and nitrogen for energy sources, in addition to nutrients for growth4. Research into how we can best harness the ability of microbes to degrade SCN– may offer newer, more cost-effective and environmentally sustainable treatment solutions5. By studying biodegradation pathways of SCN– in laboratory and field treatment bioreactor systems, we can also gain fundamental insights into connections across the natural biogeochemical cycles of carbon, sulfur and nitrogen6.
Changes in the deep subsurface microbial biosphere resulting from a field-scale CO2 geosequestration experiment
Publisher: Frontiers Media SA
Date: 14-05-2014
Biodegradation of thiocyanate by a novel strain of Burkholderia phytofirmans from soil contaminated by gold mine tailings
Publisher: Oxford University Press (OUP)
Date: 22-07-2013
DOI: 10.1111/LAM.12123
Abstract: A novel B. phytofirmans strain with the capacity to degrade thiocyanate was isolated from pH approximately 6·5 soil contaminated by effluent from gold mine tailings. This Burkholderia strain uses thiocyanate as its sole nitrogen source and can grow on acetate as a sole carbon source in a minimal medium. While biodegradation of thiocyanate has been reported to occur within alkaline environments (e.g. soda lakes and wastewater from coking plants), this work presents the first observation of thiocyanate degradation by Burkholderia at pH <9·0. Our findings therefore inform remediation strategies for thiocyanate contamination in nonalkaline soils and waters impacted by gold-mining activities. This work describes thiocyanate biodegradation by a novel Burkholderia phytofirmans strain isolated from circumneutral pH gold mining-contaminated soils. Previous reports of bacterial thiocyanate degradation have mainly focused on alkaline environments or culturing conditions (pH ≥ 9). Because cyanidation is used globally in gold mining, with thiocyanate as the major contaminant, our results will interest those working on biotechnological approaches to gold mine waste remediation.
Biodegradation of thiocyanate by a native groundwater microbial consortium
Publisher: PeerJ
Date: 26-03-2019
DOI: 10.7717/PEERJ.6498
Abstract: Gold ore processing typically generates large amounts of thiocyanate (SCN − )-contaminated effluent. When this effluent is stored in unlined tailings dams, contamination of the underlying aquifer can occur. The potential for bioremediation of SCN − -contaminated groundwater, either in situ or ex situ, remains largely unexplored. This study aimed to enrich and characterise SCN − -degrading microorganisms from mining-contaminated groundwater under a range of culturing conditions. Mildly acidic and suboxic groundwater, containing ∼135 mg L −1 SCN − , was collected from an aquifer below an unlined tailings dam. An SCN − -degrading consortium was enriched from contaminated groundwater using combinatory amendments of air, glucose and phosphate. Biodegradation occurred in all oxic cultures, except with the sole addition of glucose, but was inhibited by NH 4 + and did not occur under anoxic conditions. The SCN − -degrading consortium was characterised using 16S and 18S rRNA gene sequencing, identifying a variety of heterotrophic taxa in addition to sulphur-oxidising bacteria. Interestingly, few recognised SCN − -degrading taxa were identified in significant abundance. These results provide both proof-of-concept and the required conditions for biostimulation of SCN − degradation in groundwater by native aquifer microorganisms.
Evaluating the impacts of microbial activity and species interactions on passive bioremediation of a coastal acid sulfate soil (CASS) ecosystem
Publisher: Cold Spring Harbor Laboratory
Date: 06-07-2020
DOI: 10.1101/2020.07.04.188110
Abstract: Microbial iron and sulfate reduction are the primary drivers of coastal acid sulfate soil (CASS) passive bioremediation schemes. Microbial sulfate reduction is the limiting step for pyrite formation, a desirable endpoint for CASS remediation. Little is known, however, about the impacts of microbial activity or species interaction on long-term iron and sulfur cycling in CASS ecosystems. Using a combination of molecular biology, geochemical speciation and artificial intelligence-powered computational modeling, we deduced from microbial activity patterns (RNA-based) and geochemical measurements a best-fit equation for predicting biogeochemical pyrite formation in a model CASS ecosystem. In addition to the time-dependent activities of key sulfate-reducing prokaryotic taxa (e.g. Desulfobacteraceae ), this equation required methylotrophs ( Methylobacteriaceae ) and bacterial predators ( Bacteriovorax ) for best-fitting, suggesting that specific microbial interactions exert meaningful influences on CASS bioremediation efficiency. Our findings confirmed that CASS microorganisms act as an assemblage in response to rewetting by tidewater. Accurate predictions of long-term CASS bioremediation efficiency require modelling of complex and interdependent relationships between geochemical speciation and microbial activity. Coastal acid sulfate soil (CASS) is a global environmental issue. Microbial activity can be modelled quantitatively to predict CASS remediation. Sulfate-reducing prokaryotes (SRP) play a key role in CASS remediation. Predation on SRP with cultured representatives occurred during early wet-up. The above mechanism leads to increased activity among uncultured SRP.
Microbial contributions to coupled arsenic and sulfur cycling in the acid-sulfide hot spring Champagne Pool, New Zealand
Publisher: Frontiers Media SA
Date: 04-11-2014
Experimental evaluation of sampling, storage and analytical protocols for measuring arsenic speciation in sulphidic hot spring waters
Publisher: Elsevier BV
Date: 2017
The geomicrobiology of CO2 geosequestration: a focused review on prokaryotic community responses to field-scale CO2 injection
Publisher: Frontiers Media SA
Date: 09-04-2015
Ancient DNA from marine sediments
Publisher: Elsevier BV
Date: 09-2019
Extracellular Proteins Limit the Dispersal of Biogenic Nanoparticles
Publisher: American Association for the Advancement of Science (AAAS)
Date: 15-06-2007
Abstract: High–spatial-resolution secondary ion microprobe spectrometry, synchrotron radiation–based Fourier-transform infrared spectroscopy, and polyacrylamide gel analysis demonstrated the intimate association of proteins with spheroidal aggregates of biogenic zinc sulfide nanocrystals, an ex le of extracellular biomineralization. Experiments involving synthetic zinc sulfide nanoparticles and representative amino acids indicated a driving role for cysteine in rapid nanoparticle aggregation. These findings suggest that microbially derived extracellular proteins can limit the dispersal of nanoparticulate metal-bearing phases, such as the mineral products of bioremediation, that may otherwise be transported away from their source by subsurface fluid flow.
Impact Features on Europa: Results of the Galileo Europa Mission (GEM)
Publisher: Elsevier BV
Date: 05-2001
Subsurface carbon monoxide oxidation capacity revealed through genome‐resolved metagenomics of a carboxydotroph
Publisher: Wiley
Date: 23-07-2020
Characterization of uranium redox state in organic-rich Eocene sediments
Publisher: Elsevier BV
Date: 03-2018
DOI: 10.1016/J.CHEMOSPHERE.2017.12.012
Abstract: The presence of organic matter (OM) has a profound impact on uranium (U) redox cycling, either limiting or promoting the mobility of U via binding, reduction, or complexation. To understand the interactions between OM and U, we characterised U oxidation state and speciation in nine OM-rich sediment cores (18 s les), plus a lignite s le from the Mulga Rock polymetallic deposit in Western Australia. Uranium was unevenly dispersed within the analysed s les with 84% of the total U occurring in s les containing >21 wt % OM. Analyses of U speciation, including x-ray absorption spectroscopy and bicarbonate extractions, revealed that U existed predominately (∼71%) as U(VI), despite the low pH (4.5) and nominally reducing conditions within the sediments. Furthermore, low extractability by water, but high extractability by a bi-carbonate solution, indicated a strong association of U with particulate OM. The unexpectedly high proportion of U(VI) relative to U(IV) within the OM-rich sediments implies that OM itself does not readily reduce U, and the reduction of U is not a requirement for immobilizing uranium in OM-rich deposits. The fact that OM can play a significant role in limiting the mobility and reduction of U(VI) in sediments is important for both U-mining and remediation.
Distribution of iron- and sulfate-reducing bacteria across a coastal acid sulfate soil (CASS) environment: Implications for passive bioremediation by tidal inundation
Publisher: Frontiers Media SA
Date: 03-07-2015
Genome-resolved metagenomics and detailed geochemical speciation analyses yield new insights into microbial mercury cycling in geothermal springs
Publisher: Cold Spring Harbor Laboratory
Date: 04-02-2020
DOI: 10.1101/2020.02.03.933291
Abstract: Geothermal systems emit substantial amounts of aqueous, gaseous and methylated mercury, but little is known about microbial influences on mercury speciation. Here we report results from genome-resolved metagenomics and mercury speciation analysis of acid warm springs in the Ngawha Geothermal Field ( °C, pH 4.5), Northland Region, Aotearoa (New Zealand). Our aim was to identify the microorganisms genetically equipped for mercury methylation, demethylation, or Hg(II) reduction to volatile Hg(0) in these springs. Dissolved total and methylated mercury concentrations in two adjacent springs with different mercury speciation ranked among the highest reported from natural sources (250–16000 ng L −1 and 0.5–13.9 ng L −1 , respectively). Total solid mercury concentrations in spring sediments ranged from 1273 to 7000 µg g −1 . In the context of such ultra-high mercury levels, the geothermal microbiome was unexpectedly erse, and dominated by acidophilic and mesophilic sulfur- and iron-cycling bacteria, mercury- and arsenic-resistant bacteria, and thermophilic and acidophilic archaea. Integrating microbiome structure and metagenomic potential with geochemical constraints, we constructed a conceptual model for biogeochemical mercury cycling in geothermal springs. The model includes abiotic and biotic controls on mercury speciation, and illustrates how geothermal mercury cycling may couple to microbial community dynamics and sulfur and iron biogeochemistry. Little is currently known about biogeochemical mercury cycling in geothermal systems. This manuscript presents an important new conceptual model, supported by genome-resolved metagenomic analysis and detailed geochemical measurements. This work provides a framework for studying natural geothermal mercury emissions globally. Specifically, our findings have implications for mercury speciation in wastewaters from geothermal power plants and the potential environmental impacts of microbially and abiotically formed mercury species, particularly where mobilized in spring waters that mix with surface- or ground-waters. Furthermore, in the context of thermophilic origins for microbial mercury volatilisation, this report yields new insights into how such processes may have evolved alongside microbial mercury methylation/demethylation, and the environmental constraints imposed by the geochemistry and mineralogy of geothermal systems.
Handbook of Metal-Microbe Interactions and Bioremediation
Publisher: CRC Press
Date: 07-04-2017
Coupled nitrogen and oxygen isotope study of nitrate at a rural unlined landfill in Western Victoria, Australia
Publisher: Science Publications
Date: 04-2014
Manganese-reducing Pseudomonas fluorescens-group bacteria control arsenic mobility in gold mining-contaminated groundwater
Publisher: Springer Science and Business Media LLC
Date: 10-2014
A global perspective on microbial diversity in the terrestrial deep subsurface
Publisher: Cold Spring Harbor Laboratory
Date: 09-04-2019
DOI: 10.1101/602672
Abstract: While recent efforts to catalogue Earth’s microbial ersity have focused upon surface and marine habitats, 12% to 20% of Earth’s bacterial and archaeal biomass is suggested to inhabit the terrestrial deep subsurface, compared to ∼1.8% in the deep subseafloor 1–3 . Metagenomic studies of the terrestrial deep subsurface have yielded a trove of ergent and functionally important microbiomes from a range of localities 4–6 . However, a wider perspective of microbial ersity and its relationship to environmental conditions within the terrestrial deep subsurface is still required. Here, we show the ersity of bacterial communities in deep subsurface groundwater is controlled by aquifer lithology globally, by using 16S rRNA gene datasets collected across five countries on two continents and from fifteen rock types over the past decade. Furthermore, our meta-analysis reveals that terrestrial deep subsurface microbiota are dominated by Betaproteobacteria, Gammaproteobacteria and Firmicutes, likely as a function of the erse metabolic strategies of these taxa. Despite this similarity, evidence was found not only for aquifer-specific microbial communities, but also for a common small consortium of prevalent Betaproteobacteria and Gammaproteobacterial OTUs across the localities. This finding implies a core terrestrial deep subsurface community, irrespective of aquifer lithology, that may play an important role in colonising and sustaining microbial habitats in the deep terrestrial subsurface. An in-silico contamination-aware approach to analysing this dataset underscores the importance of downstream methods for assuring that robust conclusions can be reached from deep subsurface-derived sequencing data. Understanding the global panorama of microbial ersity and ecological dynamics in the deep terrestrial subsurface provides a first step towards understanding the role of microbes in global subsurface element and nutrient cycling.
Mercury distribution and mobility at the abandoned Puhipuhi mercury mine, Northland, New Zealand
Publisher: Informa UK Limited
Date: 02-01-2015
In Situ Stimulation of Thiocyanate Biodegradation through Phosphate Amendment in Gold Mine Tailings Water
Publisher: American Chemical Society (ACS)
Date: 08-11-2017
Abstract: Thiocyanate (SCN
Thermoflavifilum aggregans gen. nov., sp. nov., a thermophilic and slightly halophilic filamentous bacterium from the phylum Bacteroidetes
Publisher: Microbiology Society
Date: 04-2014
Abstract: A strictly aerobic, thermophilic, moderately acidophilic, non-spore-forming bacterium, strain P373 T , was isolated from geothermally heated soil at Waikite, New Zealand. Cells were filamentous rods, 0.2–0.4 µm in diameter and grew in chains up to 80 µm in length. On the basis of 16S rRNA gene sequence similarity, strain P373 T was shown to belong to the family Chitinophagaceae (class Sphingobacteriia ) of the phylum Bacteroidetes , with the most closely related cultivated strain, Chitinophaga pinensis UQM 2034 T , having 87.6 % sequence similarity. Cells stained Gram-negative, and were catalase- and oxidase-positive. The major fatty acids were i-15 : 0 (10.8 %), i-17 : 0 (24.5 %) and i-17 : 0 3-OH (35.2 %). Primary lipids were phosphatidylethanolamine, two unidentified aminolipids and three other unidentified polar lipids. The presence of sulfonolipids ( N -acyl-capnines) was observed in the total lipid extract by mass spectrometry. The G+C content of the genomic DNA was 47.3 mol% and the primary respiratory quinone was MK-7. Strain P373 T grew at 35–63 °C with an optimum temperature of 60 °C, and at pH 5.5–8.7 with an optimum growth pH of 7.3–7.4. NaCl tolerance was up to 5 % (w/v) with an optimum of 0.1–0.25 % (w/v). Cell colonies were non-translucent and pigmented vivid yellow–orange. Cells displayed an oxidative chemoheterotrophic metabolism. The distinct phylogenetic position and the phenotypic characteristics separate strain P373 T from all other members of the phylum Bacteroidetes and indicate that it represents a novel species in a new genus, for which the name Thermoflavifilum aggregans gen. nov., sp. nov. is proposed. The type strain of the type species is P373 T ( = ICMP 20041 T = DSM 27268 T ).
New insights into the genetic and metabolic diversity of thiocyanate-degrading microbial consortia
Publisher: Springer Science and Business Media LLC
Date: 23-11-2016
DOI: 10.1007/S00253-015-7161-5
Abstract: Thiocyanate is a common contaminant of the gold mining and coal coking industries for which biological degradation generally represents the most viable approach to remediation. Recent studies of thiocyanate-degrading bioreactor systems have revealed new information on the structure and metabolic activity of thiocyanate-degrading microbial consortia. Previous knowledge was limited primarily to pure-culture or co-culture studies in which the effects of linked carbon, sulfur and nitrogen cycling could not be fully understood. High throughput sequencing, DNA fingerprinting and targeted gene lification have now elucidated the genetic and metabolic ersity of these complex microbial consortia. Specifically, this has highlighted the roles of key consortium members involved in sulfur oxidation and nitrification. New insights into the biogeochemical cycling of sulfur and nitrogen in bioreactor systems allow tailoring of the microbial metabolism towards meeting effluent composition requirements. Here we review these rapidly advancing studies and synthesize a conceptual model to inform new biotechnologies for thiocyanate remediation.
Mercury methylation by metabolically versatile and cosmopolitan marine bacteria
Publisher: Cold Spring Harbor Laboratory
Date: 04-06-2020
DOI: 10.1101/2020.06.03.132969
Abstract: Microbes transform aqueous mercury (Hg) into methylmercury (MeHg), a potent neurotoxin in terrestrial and marine food webs. This process requires the gene pair hgcAB , which encodes for proteins that actuate Hg methylation, and has been well described for anoxic environments. However, recent studies report potential MeHg formation in suboxic seawater, although the microorganisms involved remain poorly understood. In this study, we conducted large-scale multi-omic analyses to search for putative microbial Hg methylators along defined redox gradients in Saanich Inlet (SI), British Columbia, a model natural ecosystem with previously measured Hg and MeHg concentration profiles. Analysis of gene expression profiles along the redoxcline identified several putative Hg methylating microbial groups, including Calditrichaeota , SAR324 and Marinimicrobia , with the last by far the most active based on hgc transcription levels. Marinimicrobia hgc genes were identified from multiple publicly available marine metagenomes, consistent with a potential key role in marine Hg methylation. Computational homology modelling predicted that Marinimicrobia HgcAB proteins contain the highly conserved structures required for functional Hg methylation. Furthermore, a number of terminal oxidases from aerobic respiratory chains were associated with several SI putative novel Hg methylators. Our findings thus reveal potential novel marine Hg-methylating microorganisms with a greater oxygen tolerance and broader habitat range than previously recognised.
Characterization of an autotrophic bioreactor microbial consortium degrading thiocyanate
Publisher: Springer Science and Business Media LLC
Date: 16-05-2017
DOI: 10.1007/S00253-017-8313-6
Abstract: Thiocyanate (SCN
The effect of heavy metals on thiocyanate biodegradation by an autotrophic microbial consortium enriched from mine tailings
Publisher: Springer Science and Business Media LLC
Date: 02-12-2020
DOI: 10.1007/S00253-020-10983-4
Abstract: Bioremediation systems represent an environmentally sustainable approach to degrading industrially generated thiocyanate (SCN − ), with low energy demand and operational costs and high efficiency and substrate specificity. However, heavy metals present in mine tailings effluent may h er process efficiency by poisoning thiocyanate-degrading microbial consortia. Here, we experimentally tested the tolerance of an autotrophic SCN − -degrading bacterial consortium enriched from gold mine tailings for Zn, Cu, Ni, Cr, and As. All of the selected metals inhibited SCN − biodegradation to different extents, depending on concentration. At pH of 7.8 and 30 °C, complete inhibition of SCN − biodegradation by Zn, Cu, Ni, and Cr occurred at 20, 5, 10, and 6 mg L −1 , respectively. Lower concentrations of these metals decreased the rate of SCN − biodegradation, with relatively long lag times. Interestingly, the microbial consortium tolerated As even at 500 mg L −1 , although both the rate and extent of SCN − biodegradation were affected. Potentially, the observed As tolerance could be explained by the origin of our microbial consortium in tailings derived from As-enriched gold ore (arsenopyrite). This study highlights the importance of considering metal co-contamination in bioreactor design and operation for SCN − bioremediation at mine sites. • Both the efficiency and rate of SCN − biodegradation were inhibited by heavy metals, to different degrees depending on type and concentration of metal. • The autotrophic microbial consortium was capable of tolerating high concentrations of As, potential having adapted to higher As levels derived from the tailings source.
Microbial mercury methylation in Antarctic sea ice
Publisher: Springer Science and Business Media LLC
Date: 08-2016
DOI: 10.1038/NMICROBIOL.2016.127
Abstract: Atmospheric deposition of mercury onto sea ice and circumpolar sea water provides mercury for microbial methylation, and contributes to the bioaccumulation of the potent neurotoxin methylmercury in the marine food web. Little is known about the abiotic and biotic controls on microbial mercury methylation in polar marine systems. However, mercury methylation is known to occur alongside photochemical and microbial mercury reduction and subsequent volatilization. Here, we combine mercury speciation measurements of total and methylated mercury with metagenomic analysis of whole-community microbial DNA from Antarctic snow, brine, sea ice and sea water to elucidate potential microbially mediated mercury methylation and volatilization pathways in polar marine environments. Our results identify the marine microaerophilic bacterium Nitrospina as a potential mercury methylator within sea ice. Anaerobic bacteria known to methylate mercury were notably absent from sea-ice metagenomes. We propose that Antarctic sea ice can harbour a microbial source of methylmercury in the Southern Ocean.
Mercury methylation by metabolically versatile and cosmopolitan marine bacteria
Publisher: Springer Science and Business Media LLC
Date: 27-01-2021
DOI: 10.1038/S41396-020-00889-4
Abstract: Microbes transform aqueous mercury (Hg) into methylmercury (MeHg), a potent neurotoxin that accumulates in terrestrial and marine food webs, with potential impacts on human health. This process requires the gene pair hgcAB , which encodes for proteins that actuate Hg methylation, and has been well described for anoxic environments. However, recent studies report potential MeHg formation in suboxic seawater, although the microorganisms involved remain poorly understood. In this study, we conducted large-scale multi-omic analyses to search for putative microbial Hg methylators along defined redox gradients in Saanich Inlet, British Columbia, a model natural ecosystem with previously measured Hg and MeHg concentration profiles. Analysis of gene expression profiles along the redoxcline identified several putative Hg methylating microbial groups, including Calditrichaeota, SAR324 and Marinimicrobia, with the last the most active based on hgc transcription levels. Marinimicrobia hgc genes were identified from multiple publicly available marine metagenomes, consistent with a potential key role in marine Hg methylation. Computational homology modelling predicts that Marinimicrobia HgcAB proteins contain the highly conserved amino acid sites and folding structures required for functional Hg methylation. Furthermore, a number of terminal oxidases from aerobic respiratory chains were associated with several putative novel Hg methylators. Our findings thus reveal potential novel marine Hg-methylating microorganisms with a greater oxygen tolerance and broader habitat range than previously recognized.
The effect of heavy metals on thiocyanate biodegradation by an autotrophic microbial consortium enriched from mine tailings
Publisher: Cold Spring Harbor Laboratory
Date: 13-06-2020
DOI: 10.1101/2020.06.13.149401
Abstract: Bioremediation systems represent an environmentally sustainable approach to degrading industrially-generated thiocyanate (SCN - ), with low energy demand and operational costs, and high efficiency and substrate specificity. However, heavy metals present in mine tailings effluent may h er process efficiency by poisoning thiocyanate-degrading microbial consortia. Here we experimentally tested the tolerance of an autotrophic SCN - -degrading bacterial consortium enriched from gold mine tailings for Zn, Cu, Ni, Cr, and As. All of the selected metals inhibited SCN - biodegradation to different extents, depending on concentration. At pH of 7.8 and 30°C, complete inhibition of SCN - biodegradation by Zn, Cu, Ni, and Cr occurred at 20, 5, 10, and 6 mg L -1 , respectively. Lower concentrations of these metals decreased the rate of SCN - biodegradation, with relatively long lag times. Interestingly, the microbial consortium tolerated As even at 500 mg L -1 , although both the rate and extent of SCN - biodegradation were affected. This study highlights the importance of considering metal co-contamination in bioreactor design and operation for SCN - bioremediation at mine sites. Both the efficiency and rate of SCN - biodegradation were inhibited by heavy metals, to different degrees depending on type and concentration of metal The autotrophic microbial consortium was capable of tolerating high levels of As
A consensus protocol for the recovery of mercury methylation genes from metagenomes
Publisher: Cold Spring Harbor Laboratory
Date: 14-03-2022
DOI: 10.1101/2022.03.14.484253
Abstract: Mercury methylation genes ( hgcAB) mediate the formation of the toxic methylmercury and have been identified from erse environments, including freshwater and marine ecosystems, Arctic permafrost, forest and paddy soils, coal-ash amended sediments, chlor-alkali plants discharges and geothermal springs. Here we present the first attempt at a standardized protocol for the detection, identification and quantification of hgc genes from metagenomes. Our Hg-MATE (Hg-cycling Microorganisms in Aquatic and Terrestrial Ecosystems) database, a catalogue of hgc genes, provides the most accurate information to date on the taxonomic identity and functional/metabolic attributes of microorganisms responsible for Hg methylation in the environment. Furthermore, we introduce “marky-coco”, a ready-to-use bioinformatic pipeline based on de novo single-metagenome assembly, for easy and accurate characterization of hgc genes from environmental s les. We compared the recovery of hgc genes from environmental metagenomes using the marky-coco pipeline with an approach based on co-assembly of multiple metagenomes. Our data show similar efficiency in both approaches for most environments except those with high ersity (i.e., paddy soils) for which a co-assembly approach was preferred. Finally, we discuss the definition of true hgc genes and methods to normalize hgc gene counts from metagenomes.
Time-resolved microbial guild responses to tidal cycling in a coastal acid-sulfate system
Publisher: CSIRO Publishing
Date: 2018
DOI: 10.1071/EN16203
Abstract: Environmental contextMicrobes play key roles in controlling acidification and metal toxicity in coastal acid-sulfate soils. We characterised the time-dependent metabolic activities of abundant and rare taxa in acidifying tidal wetlands and showed that rare taxa exhibiting higher activity may exert significant influence on iron- and sulfur-cycling. Our findings yield new insights into the drivers and timing of iron- and sulfur-cycling in coastal acid-sulfate systems. AbstractTidal inundation has been trialled as a remediation strategy for coastal acid-sulfate soil (CASS) environments. Microbial community structure and activity are hypothesised to play key roles in this process, but remain poorly understood for long-term (decadal or longer) CASS ecosystems. More detailed understanding of the distribution and timing of microbial activity in CASS ecosystems is necessary to evaluate their real bioremediation potential. In this study, we compared 16S ribosomal DNA (rRNA) and RNA (as copy DNA, cDNA, a proxy for overall enzymatic activity) sequence datasets to characterise and resolve microbial community structure and activity across a tidal cycle in the East Trinity long-term CASS wetland (Queensland, Australia). The timing and extent of activity among abundant ( %) and rare ( .1 %) microbial taxa showed that a larger number of rare members (phylotype) displayed greater overall range in activity than was apparent for more abundant members. Certain taxa from both abundant and rare populations varied rapidly in their 16S rRNA levels in response to tidal cycling. The observation of rRNA accumulation in response to drying and rewetting was used to ide the microbial community structure into ‘early responders’ (within 3 h of dry-down or wet-up) and ‘delayed responders’ (3+ h after wet-up). Response patterns were phylogenetically constrained across supra- to subtidal zones across all tidal stages. Microbial iron- and sulfur-cycling networks included these rare but active taxa, illustrating their spatiotemporal complexity, which should be considered for an accurate assessment of bioremediation efficiency, and specially for validating predictive biogeochemical models of long-term CASS ecosystems.
Mercury sources, distribution, and bioavailability in the North Pacific Ocean: Insights from data and models
Publisher: American Geophysical Union (AGU)
Date: 05-2009
DOI: 10.1029/2008GB003425
The effect of natural organic matter on mercury methylation by Desulfobulbus propionicus 1pr3
Publisher: Frontiers Media SA
Date: 18-12-2015
A consensus protocol for the recovery of mercury methylation genes from metagenomes
Publisher: Wiley
Date: 04-08-2022
Abstract: Mercury (Hg) methylation genes ( hgcAB ) mediate the formation of the toxic methylmercury and have been identified from erse environments, including freshwater and marine ecosystems, Arctic permafrost, forest and paddy soils, coal‐ash amended sediments, chlor‐alkali plants discharges and geothermal springs. Here we present the first attempt at a standardized protocol for the detection, identification and quantification of hgc genes from metagenomes. Our Hg‐cycling microorganisms in aquatic and terrestrial ecosystems (Hg‐MATE) database, a catalogue of hgc genes, provides the most accurate information to date on the taxonomic identity and functional/metabolic attributes of microorganisms responsible for Hg methylation in the environment. Furthermore, we introduce “marky‐coco”, a ready‐to‐use bioinformatic pipeline based on de novo single‐metagenome assembly, for easy and accurate characterization of hgc genes from environmental s les. We compared the recovery of hgc genes from environmental metagenomes using the marky‐coco pipeline with an approach based on coassembly of multiple metagenomes. Our data show similar efficiency in both approaches for most environments except those with high ersity (i.e., paddy soils) for which a coassembly approach was preferred. Finally, we discuss the definition of true hgc genes and methods to normalize hgc gene counts from metagenomes.
Metagenomic and lipid analyses reveal a diel cycle in a hypersaline microbial ecosystem
Publisher: Springer Science and Business Media LLC
Date: 28-04-2015
Thermorudis pharmacophila sp. nov., a novel member of the class Thermomicrobia isolated from geothermal soil, and emended descriptions of Thermomicrobium roseum, Thermomicrobium carboxidum, Thermoru
Publisher: Microbiology Society
Date: 12-2015
Abstract: An aerobic, thermophilic and cellulolytic bacterium, designated strain WKT50.2 T , was isolated from geothermal soil at Waikite, New Zealand. Strain WKT50.2 T grew at 53–76 °C and at pH 5.9–8.2. The DNA G+C content was 58.4 mol%. The major fatty acids were 12-methyl C 18 : 0 and C 18 : 0 . Polar lipids were all linked to long-chain 1,2-diols, and comprised 2-acylalkyldiol-1- O -phosphoinositol (diolPI), 2-acylalkyldiol-1- O -phosphoacylmannoside (diolP-acylMan), 2-acylalkyldiol-1- O -phosphoinositol acylmannoside (diolPI-acylMan) and 2-acylalkyldiol-1- O -phosphoinositol mannoside (diolPI-Man). Strain WKT50.2 T utilized a range of cellulosic substrates, alcohols and organic acids for growth, but was unable to utilize monosaccharides. Robust growth of WKT50.2 T was observed on protein derivatives. WKT50.2 T was sensitive to icillin, chlor henicol, kanamycin, neomycin, polymyxin B, streptomycin and vancomycin. Metronidazole, lasalocid A and trimethoprim stimulated growth. Phylogenetic analysis of 16S rRNA gene sequences showed that WKT50.2 T belonged to the class Thermomicrobia within the phylum Chloroflexi , and was most closely related to Thermorudis peleae KI4 T (99.6% similarity). DNA–DNA hybridization between WKT50.2 T and Thermorudis peleae DSM 27169 T was 18.0%. Physiological and biochemical tests confirmed the phenotypic and genotypic differentiation of strain WKT50.2 T from Thermorudis peleae KI4 T and other members of the Thermomicrobia . On the basis of its phylogenetic position and phenotypic characteristics, we propose that strain WKT50.2 T represents a novel species, for which the name Thermorudis pharmacophila sp. nov. is proposed, with the type strain WKT50.2 T ( = DSM 26011 T = ICMP 20042 T ). Emended descriptions of Thermomicrobium roseum , Thermomicrobium carboxidum , Thermorudis peleae and Sphaerobacter thermophilus are also proposed, and include the description of a novel respiratory quinone, MK-8 2,3-epoxide (23%), in Thermomicrobium roseum .
Quantifying Heavy Metals Sequestration by Sulfate-Reducing Bacteria in an Acid Mine Drainage-Contaminated Natural Wetland
Publisher: Frontiers Media SA
Date: 2013
Seawater recirculation through subducting sediments sustains a deeply buried population of sulfate-reducing bacteria.
Publisher: Wiley
Date: 25-11-2018
DOI: 10.1111/GBI.12324
Abstract: Subseafloor sulfate concentrations typically decrease with depth as this electron acceptor is consumed by respiring microorganisms. However, studies show that seawater can flow through hydraulically conductive basalt to deliver sulfate upwards into deeply buried overlying sediments. Our previous work on IODP Site C0012A (Nankai Trough, Japan) revealed that recirculation of sulfate through the subducting Philippine Sea Plate stimulated microbial activity near the sediment-basement interface (SBI). Here, we describe the microbial ecology, phylogeny, and energetic requirements of population of aero-tolerant sulfate-reducing bacteria in the deep subseafloor. We identified dissimilatory sulfite reductase gene (dsr) sequences 93% related to oxygen-tolerant Desulfovibrionales species across all reaction zones while no SRB were detected in drilling fluid control s les. Pore fluid chemistry revealed low concentrations of methane (<0.25 mM), while hydrogen levels were consistent with active bacterial sulfate reduction (0.51-1.52 nM). Solid phase total organic carbon (TOC) was also considerably low in these subseafloor sediments. Our results reveal the phylogenetic ersity, potential function, and physiological tolerance of a community of sulfate-reducing bacteria living at ~480 m below subducting seafloor.
Genome-Resolved Metagenomics and Detailed Geochemical Speciation Analyses Yield New Insights into Microbial Mercury Cycling in Geothermal Springs
Publisher: American Society for Microbiology
Date: 20-07-2020
DOI: 10.1128/AEM.00176-20
Abstract: Little is currently known about biogeochemical mercury cycling in geothermal systems. The manuscript presents a new conceptual model, supported by genome-resolved metagenomic analysis and detailed geochemical measurements. The model illustrates environmental factors that influence mercury cycling in acidic springs, including transitions between solid (mineral) and aqueous phases of mercury, as well as the interconnections among mercury, sulfur, and iron cycles. This work provides a framework for studying natural geothermal mercury emissions globally. Specifically, our findings have implications for mercury speciation in wastewaters from geothermal power plants and the potential environmental impacts of microbially and abiotically formed mercury species, particularly where they are mobilized in spring waters that mix with surface or groundwaters. Furthermore, in the context of thermophilic origins for microbial mercury volatilization, this report yields new insights into how such processes may have evolved alongside microbial mercury methylation/demethylation and the environmental constraints imposed by the geochemistry and mineralogy of geothermal systems.
Effects of Environmental Parameters on Thiocyanate Biodegradation by Burkholderia phytofirmans Candidate Strain ST01hv
Publisher: Mary Ann Liebert Inc
Date: 2018
Genome-resolved metagenomics of an autotrophic thiocyanate-remediating microbial bioreactor consortium
Publisher: Elsevier BV
Date: 07-2019
DOI: 10.1016/J.WATRES.2019.02.058
Abstract: Industrial thiocyanate (SCN
Limisphaera ngatamarikiensis gen. nov., sp. nov., a thermophilic, pink-pigmented coccus isolated from subaqueous mud of a geothermal hotspring
Publisher: Microbiology Society
Date: 04-2015
DOI: 10.1099/IJS.0.000063
Abstract: A novel bacterial strain, NGM72.4 T , was isolated from a hot spring in the Ngatamariki geothermal field, New Zealand. Phylogenetic analysis based on 16S rRNA gene sequences grouped it into the phylum Verrucomicrobia and class level group 3 (also known as OPB35 soil group). NGM72.4 T stained Gram-negative, and was catalase- and oxidase-positive. Cells were small cocci, 0.5–0.8 µm in diameter, which were motile by means of single flagella. Transmission electron micrograph (TEM) imaging showed an unusual pirellulosome-like intracytoplasmic membrane. The peptidoglycan content was very small with only trace levels of diaminopimelic acid detected. No peptidoglycan structure was visible in TEM imaging. The predominant isoprenoid quinone was MK-7 (92 %). The major fatty acids ( %) were C 16 : 0 , anteiso-C 15 : 0 , iso-C 16 : 0 and anteiso-C 17 : 0 . Major phospholipids were phosphatidylethanolamine (PE), phosphatidylmonomethylethanolamine (PMME) and cardiolipin (CL), and a novel analogous series of phospholipids where diacylglycerol was replaced with diacylserinol (sPE, sPMME, sCL). The DNA G+C content was 65.6 mol%. Cells displayed an oxidative chemoheterotrophic metabolism. NGM72.4 T is a strictly aerobic thermophile (growth optimum 60–65 °C), has a slightly alkaliphilic pH growth optimum (optimum pH 8.1–8.4) and has a NaCl tolerance of up to 8 g l −1 . Colonies were small, circular and pigmented pale pink. The distinct phylogenetic position and phenotypic traits of strain NGM72.4 T distinguish it from all other described species of the phylum Verrucomicrobia and, therefore, it is considered to represent a novel species in a new genus for which we propose the name Limisphaera ngatamarikiensis gen. nov., sp. nov. The type strain is NGM72.4 T ( = ICMP 20182 T = DSM 27329 T ).
On the origin and evolution of microbial mercury methylation
Publisher: Cold Spring Harbor Laboratory
Date: 24-11-2022
DOI: 10.1101/2022.11.21.517362
Abstract: The origin of microbial mercury methylation has long been a mystery. Here we employed genome-resolved phylogenetic analyses to decipher the evolution of the mercury methylating gene, hgcAB , constrain the ancestral origin of the hgc operon, and explain the distribution of hgc in Bacteria and Archaea. We infer the extent to which vertical inheritance and horizontal gene transfer have influenced the evolution of mercury methylators and hypothesize that evolution of this trait bestowed the ability to produce an antimicrobial compound (MeHg + ) on a potentially resource-limited early Earth. We speculate that, in response, the evolution of MeHg + -detoxifying alkylmercury lyase (encoded by merB ) reduced a selective advantage for mercury methylators and resulted in widespread loss of hgc in Bacteria and Archaea. Neurotoxic methylmercury (MeHg + (aq) ) is synthesized from Hg II (aq) in the environment by microorganisms possessing the gene pair hgcAB . Our phylogenetic analyses elucidate the origin and evolution of the hgc operon, and support a hypothesis that mercury methylation evolved as an antimicrobial production mechanism, possibly from competition for limited resources on the early Earth. We infer from our analyses that hgc has been primarily vertically inherited in Bacteria and Archaea, with extensive parallel loss, and note that few taxa possessing hgc also possess the gene encoding for MeHg + demethylation, merB . Our findings support the interpretation that merB evolved as a defense mechanism against the evolution of microbial Hg II (aq) methylation.
Thiocyanate adsorption on ferrihydrite and its fate during ferrihydrite transformation to hematite and goethite
Publisher: Elsevier BV
Date: 2015
DOI: 10.1016/J.CHEMOSPHERE.2014.09.019
Abstract: Thiocyanate (SCN(-)) is a toxic contaminant produced by industrial processes such as gold ore cyanidation and coal coking. The potential for remediation by adsorption of SCN(-) on ferrihydrite, the influence of sulfate (SO4(2-)) on SCN(-) adsorption, and the fate of adsorbed SCN(-) during ferrihydrite aging were studied using macroscopic techniques complemented with attenuated total reflectance-Fourier transform infrared analysis (ATR-FTIR), X-ray powder diffraction (XRD) and transmission electron microscopy (TEM). Results showed that adsorption of SCN(-) was strongly affected by the concentration of electrolyte (NaNO3) and pH, with decreases in concentration of NaNO3 and pH leading to increased SCN(-) adsorption. The adsorption isotherms can be described by the Langmuir model. While at lower concentrations (0.52-1.04 mM), the presence of SO4(2-) had little impact on SCN(-) adsorption, at a higher concentration (2.08 mM), SCN(-) adsorption was significantly inhibited. ATR-FTIR data confirmed that SCN(-) was bound as an outer-sphere complex on ferrihydrite, and this mechanism was not influenced by changes in pH or electrolyte concentration. XRD data showed that ferrihydrite transformed to a mixture of hematite and goethite at 75 °C and pH 5 in the presence and absence of SCN(-). Partitioning data revealed that during ferrihydrite transformation, all adsorbed SCN(-) was released into solution.
Biodegradation of thiocyanate in groundwater by a native aquifer microbial consortium
Publisher: PeerJ
Date: 03-01-2018
DOI: 10.7287/PEERJ.PREPRINTS.3503V1
Abstract: Gold ore processing typically generates large amounts of thiocyanate (SCN - )-contaminated effluent. When this effluent is stored in unlined tailings dams, contamination of the underlying aquifer can occur. The potential for bioremediation of SCN - -contaminated groundwater, either in situ or through ex situ , remains largely unexplored. This study aimed to enrich and characterise SCN - -degrading microorganisms from mining-contaminated groundwater under a range of culturing conditions. Mildly acidic and suboxic groundwater, containing ~135 mgL -1 SCN - , was collected from an aquifer below an unlined tailings dam. An SCN - -degrading consortium was enriched from contaminated groundwater using combinatory amendments of air, glucose and phosphate. Biodegradation occurred in all oxic cultures, except with the sole addition of glucose, but was inhibited by NH 4 + and did not occur under anoxic conditions. The SCN - -degrading consortium was characterised using 16S and 18S rRNA gene sequencing, identifying a variety of heterotrophic taxa in addition to sulfur-oxidising bacteria. Interestingly, few recognised SCN - -degrading taxa were identified in significant abundance. These results provide both proof-of-concept and the required conditions for biostimulation of SCN - degradation in groundwater by native aquifer microorganisms.
Uranium mobility in organic matter-rich sediments: A review of geological and geochemical processes
Publisher: Elsevier BV
Date: 08-2016
Crustal fluid and ash alteration impacts on the biosphere of Shikoku Basin sediments, Nankai Trough, Japan
Publisher: Wiley
Date: 17-06-2015
DOI: 10.1111/GBI.12146
Abstract: We present data from sediment cores collected from IODP Site C0012 in the Shikoku Basin. Our site lies at the Nankai Trough, just prior to subduction of the 19 Ma Philippine Sea plate. Our data indicate that the sedimentary package is undergoing multiple routes of electron transport and that these differing pathways for oxidant supply generate a complex array of metabolic routes and microbial communities involved in carbon cycling. Numerical simulations matched to pore water data document that Ca(2+) and Cl(1-) are largely supplied via diffusion from a high-salinity (44.5 psu) basement fluid, which supports the presence of halophile Archean communities within the deep sedimentary package that are not observed in shallow sediments. Sulfate supply from basement supports anaerobic oxidation of methane (AOM) at a rate of ~0.2 pmol cm(-3) day(-1) at ~400 mbsf. We also note the disappearance of δ-Proteobacteria at 434 mbsf, coincident with the maximum in methane concentration, and their reappearance at 463 mbsf, coinciding with the observed deeper increase in sulfate concentration toward the basement. We did not, however, find ANME representatives in any of the s les analyzed (from 340 to 463 mbsf). The lack of ANME may be due to an overshadowing effect from the more dominant archaeal phylotypes or may indicate involvement of unknown groups of archaea in AOM (i.e., unclassified Euryarchaeota). In addition to the supply of sulfate from a basement aquifer, the deep biosphere at this site is also influenced by an elevated supply of reactive iron (up to 143 μmol g(-1)) and manganese (up to 20 μmol g(-1)). The effect of these metal oxides on the sulfur cycle is inferred from an accompanying sulfur isotope fractionation much smaller than expected from traditional sulfate-reducing pathways. The detection of the manganese- and iron-reducer γ-Proteobacteria Alteromonas at 367 mbsf is consistent with these geochemical inferences.
Diversity of Dissimilatory Sulfite Reductase Genes ( dsrAB ) in a Salt Marsh Impacted by Long-Term Acid Mine Drainage
Publisher: American Society for Microbiology
Date: 15-07-2010
DOI: 10.1128/AEM.03006-09
Abstract: Sulfate-reducing bacteria (SRB) play a major role in the coupled biogeochemical cycling of sulfur and chalcophilic metal(loid)s. By implication, they can exert a strong influence on the speciation and mobility of multiple metal(loid) contaminants. In this study, we combined DsrAB gene sequencing and sulfur isotopic profiling to identify the phylogeny and distribution of SRB and to assess their metabolic activity in salt marsh sediments exposed to acid mine drainage (AMD) for over 100 years. Recovered dsrAB sequences from three sites s led along an AMD flow path indicated the dominance of a single Desulfovibrio species. Other major sequence clades were related most closely to Desulfosarcina , Desulfococcus , Desulfobulbus , and Desulfosporosinus species. The presence of metal sulfides with low δ 34 S values relative to δ 34 S values of pore water sulfate showed that sediment SRB populations were actively reducing sulfate under ambient conditions (pH of ∼2), although possibly within less acidic microenvironments. Interestingly, δ 34 S values for pore water sulfate were lower than those for sulfate delivered during tidal inundation of marsh sediments. 16S rRNA gene sequence data from sediments and sulfur isotope data confirmed that sulfur-oxidizing bacteria drove the reoxidation of biogenic sulfide coupled to oxygen or nitrate reduction over a timescale of hours. Collectively, these findings imply a highly dynamic microbially mediated cycling of sulfate and sulfide, and thus the speciation and mobility of chalcophilic contaminant metal(loid)s, in AMD-impacted marsh sediments.
Related Organisations
University Of Glasgow
Location: United Kingdom of Great Britain and Northern Ireland
University Of California, Berkeley
Location: United States of America
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