1
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Voutsinos MY, West-Roberts JA, Sachdeva R, Moreau JW, Banfield JF. Weathered granites and soils harbour microbes with lanthanide-dependent methylotrophic enzymes. BMC Biol 2024; 22:41. [PMID: 38369453 PMCID: PMC10875860 DOI: 10.1186/s12915-024-01841-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2023] [Accepted: 02/07/2024] [Indexed: 02/20/2024] Open
Abstract
BACKGROUND Prior to soil formation, phosphate liberated by rock weathering is often sequestered into highly insoluble lanthanide phosphate minerals. Dissolution of these minerals releases phosphate and lanthanides to the biosphere. Currently, the microorganisms involved in phosphate mineral dissolution and the role of lanthanides in microbial metabolism are poorly understood. RESULTS Although there have been many studies of soil microbiology, very little research has investigated microbiomes of weathered rock. Here, we sampled weathered granite and associated soil to identify the zones of lanthanide phosphate mineral solubilisation and genomically define the organisms implicated in lanthanide utilisation. We reconstructed 136 genomes from 11 bacterial phyla and found that gene clusters implicated in lanthanide-based metabolism of methanol (primarily xoxF3 and xoxF5) are surprisingly common in microbial communities in moderately weathered granite. Notably, xoxF3 systems were found in Verrucomicrobia for the first time, and in Acidobacteria, Gemmatimonadetes and Alphaproteobacteria. The xoxF-containing gene clusters are shared by diverse Acidobacteria and Gemmatimonadetes, and include conserved hypothetical proteins and transporters not associated with the few well studied xoxF systems. Given that siderophore-like molecules that strongly bind lanthanides may be required to solubilise lanthanide phosphates, it is notable that candidate metallophore biosynthesis systems were most prevalent in bacteria in moderately weathered rock, especially in Acidobacteria with lanthanide-based systems. CONCLUSIONS Phosphate mineral dissolution, putative metallophore production and lanthanide utilisation by enzymes involved in methanol oxidation linked to carbonic acid production co-occur in the zone of moderate granite weathering. In combination, these microbial processes likely accelerate the conversion of granitic rock to soil.
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Affiliation(s)
- Marcos Y Voutsinos
- School of Geography, Earth and Atmospheric Sciences, The University of Melbourne, Melbourne, VIC, Australia
- Department of Microbiology, Biomedicine Discovery Institute, Monash University, Melbourne, Australia
| | - Jacob A West-Roberts
- Department of Environmental Science, Policy and Management, University of California, Berkeley, CA, USA
| | - Rohan Sachdeva
- Department of Earth and Planetary Science, University of California, Berkeley, CA, USA
| | - John W Moreau
- School of Geographical and Earth Sciences, University of Glasgow, Glasgow, UK
| | - Jillian F Banfield
- School of Geography, Earth and Atmospheric Sciences, The University of Melbourne, Melbourne, VIC, Australia.
- Department of Microbiology, Biomedicine Discovery Institute, Monash University, Melbourne, Australia.
- Department of Environmental Science, Policy and Management, University of California, Berkeley, CA, USA.
- Department of Earth and Planetary Science, University of California, Berkeley, CA, USA.
- Innovative Genomics Institute, University of California Berkeley, Berkeley, CA, USA.
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2
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Power JF, Carere CR, Welford HE, Hudson DT, Lee KC, Moreau JW, Ettema TJG, Reysenbach AL, Lee CK, Colman DR, Boyd ES, Morgan XC, McDonald IR, Craig Cary S, Stott MB. A genus in the bacterial phylum Aquificota appears to be endemic to Aotearoa-New Zealand. Nat Commun 2024; 15:179. [PMID: 38167814 PMCID: PMC10762115 DOI: 10.1038/s41467-023-43960-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2023] [Accepted: 11/24/2023] [Indexed: 01/05/2024] Open
Abstract
Allopatric speciation has been difficult to examine among microorganisms, with prior reports of endemism restricted to sub-genus level taxa. Previous microbial community analysis via 16S rRNA gene sequencing of 925 geothermal springs from the Taupō Volcanic Zone (TVZ), Aotearoa-New Zealand, revealed widespread distribution and abundance of a single bacterial genus across 686 of these ecosystems (pH 1.2-9.6 and 17.4-99.8 °C). Here, we present evidence to suggest that this genus, Venenivibrio (phylum Aquificota), is endemic to Aotearoa-New Zealand. A specific environmental niche that increases habitat isolation was identified, with maximal read abundance of Venenivibrio occurring at pH 4-6, 50-70 °C, and low oxidation-reduction potentials. This was further highlighted by genomic and culture-based analyses of the only characterised species for the genus, Venenivibrio stagnispumantis CP.B2T, which confirmed a chemolithoautotrophic metabolism dependent on hydrogen oxidation. While similarity between Venenivibrio populations illustrated that dispersal is not limited across the TVZ, extensive amplicon, metagenomic, and phylogenomic analyses of global microbial communities from DNA sequence databases indicates Venenivibrio is geographically restricted to the Aotearoa-New Zealand archipelago. We conclude that geographic isolation, complemented by physicochemical constraints, has resulted in the establishment of an endemic bacterial genus.
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Affiliation(s)
- Jean F Power
- Thermophile Research Unit, Te Aka Mātuatua | School of Science, Te Whare Wānanga o Waikato | University of Waikato, Hamilton, 3240, Aotearoa New Zealand
| | - Carlo R Carere
- Te Tari Pūhanga Tukanga Matū | Department of Chemical and Process Engineering, Te Whare Wānanga o Waitaha | University of Canterbury, Christchurch, 8140, Aotearoa New Zealand
| | - Holly E Welford
- Te Kura Pūtaiao Koiora | School of Biological Sciences, Te Whare Wānanga o Waitaha | University of Canterbury, Christchurch, 8140, Aotearoa New Zealand
| | - Daniel T Hudson
- Te Tari Moromoroiti me te Ārai Mate | Department of Microbiology and Immunology, Te Whare Wānanga o Ōtākou | University of Otago, Dunedin, 9054, Aotearoa New Zealand
| | - Kevin C Lee
- Te Kura Pūtaiao | School of Science, Te Wānanga Aronui o Tāmaki Makau Rau | Auckland University of Technology, Auckland, 1010, Aotearoa New Zealand
| | - John W Moreau
- School of Geographical & Earth Sciences, University of Glasgow, Glasgow, G12 8RZ, UK
| | - Thijs J G Ettema
- Laboratory of Microbiology, Wageningen University & Research, 6708, WE, Wageningen, the Netherlands
| | | | - Charles K Lee
- Thermophile Research Unit, Te Aka Mātuatua | School of Science, Te Whare Wānanga o Waikato | University of Waikato, Hamilton, 3240, Aotearoa New Zealand
| | - Daniel R Colman
- Department of Microbiology and Cell Biology, Montana State University, Bozeman, MT, 59717, USA
| | - Eric S Boyd
- Department of Microbiology and Cell Biology, Montana State University, Bozeman, MT, 59717, USA
| | - Xochitl C Morgan
- Te Tari Moromoroiti me te Ārai Mate | Department of Microbiology and Immunology, Te Whare Wānanga o Ōtākou | University of Otago, Dunedin, 9054, Aotearoa New Zealand
- Department of Biostatistics, Harvard T. H. Chan School of Public Health, Boston, MA, 02115, USA
| | - Ian R McDonald
- Thermophile Research Unit, Te Aka Mātuatua | School of Science, Te Whare Wānanga o Waikato | University of Waikato, Hamilton, 3240, Aotearoa New Zealand
| | - S Craig Cary
- Thermophile Research Unit, Te Aka Mātuatua | School of Science, Te Whare Wānanga o Waikato | University of Waikato, Hamilton, 3240, Aotearoa New Zealand.
| | - Matthew B Stott
- Te Kura Pūtaiao Koiora | School of Biological Sciences, Te Whare Wānanga o Waitaha | University of Canterbury, Christchurch, 8140, Aotearoa New Zealand.
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3
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Cattò C, Mu A, Moreau JW, Wang N, Cappitelli F, Strugnell R. Biofilm colonization of stone materials from an Australian outdoor sculpture: Importance of geometry and exposure. J Environ Manage 2023; 339:117948. [PMID: 37080094 DOI: 10.1016/j.jenvman.2023.117948] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/13/2023] [Revised: 03/27/2023] [Accepted: 04/12/2023] [Indexed: 05/04/2023]
Abstract
The safeguarding of Australian outdoor stone heritage is currently limited by a lack of information concerning mechanisms responsible for the degradation of the built heritage. In this study, the bacterial community colonizing the stone surface of an outdoor sculpture located at the Church of St. John the Evangelist in Melbourne was analysed, providing an overview of the patterns of microbial composition associated with stone in an anthropogenic context. Illumina MiSeq 16S rRNA gene sequencing together with confocal laser microscope investigations highlighted the bacterial community was composed of both phototrophic and chemotrophic microorganisms characteristic of stone and soil, and typical of arid, salty and urban environments. Cardinal exposure, position and surface geometry were the most important factors in determining the structure of the microbial community. The North-West exposed areas on the top of the sculpture with high light exposure gave back the highest number of sequences and were dominated by Cyanobacteria. The South and West facing in middle and lower parts of the sculpture received significantly lower levels of radiation and were dominated by Actinobacteria. Proteobacteria were observed as widespread on the sculpture. This pioneer research provided an in-depth investigation of the microbial community structure on a deteriorated artistic stone in the Australian continent and provides information for the identification of deterioration-associated microorganisms and/or bacteria beneficial for stone preservation.
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Affiliation(s)
- Cristina Cattò
- Department of Food Environmental and Nutritional Sciences, Università Degli Studi di Milano, Milano, Italy; Department of Microbiology and Immunology, At the Peter Doherty Institute for Infection and Immunity, The University of Melbourne, Melbourne, VIC, Australia.
| | - Andre Mu
- Department of Microbiology and Immunology, At the Peter Doherty Institute for Infection and Immunity, The University of Melbourne, Melbourne, VIC, Australia; Doherty Applied Microbial Genomics, Department of Microbiology and Immunology, At the Peter Doherty Institute for Infection and Immunity, The University of Melbourne, Melbourne, VIC, Australia.
| | - John W Moreau
- School of Geographical and Earth Sciences, University of Glasgow, Glasgow, United Kingdom; School of Geographical, Atmospheric and Earth Sciences, The University of Melbourne, Parkville, VIC, Australia.
| | - Nancy Wang
- Department of Microbiology and Immunology, At the Peter Doherty Institute for Infection and Immunity, The University of Melbourne, Melbourne, VIC, Australia.
| | - Francesca Cappitelli
- Department of Food Environmental and Nutritional Sciences, Università Degli Studi di Milano, Milano, Italy.
| | - Richard Strugnell
- Department of Microbiology and Immunology, At the Peter Doherty Institute for Infection and Immunity, The University of Melbourne, Melbourne, VIC, Australia.
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4
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Lin H, Moody ERR, Williams TA, Moreau JW. On the origin and evolution of microbial mercury methylation. Genome Biol Evol 2023; 15:7084592. [PMID: 36951100 PMCID: PMC10083202 DOI: 10.1093/gbe/evad051] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2022] [Revised: 03/03/2023] [Accepted: 03/14/2023] [Indexed: 03/24/2023] Open
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.
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Affiliation(s)
- Heyu Lin
- School of Geographical, Atmospheric and Earth Sciences, The University of Melbourne, Parkville, Victoria 3010, Australia
| | - Edmund R R Moody
- School of Earth Sciences, University of Bristol, Bristol, BS8 1RJ, United Kingdom
| | - Tom A Williams
- School of Biological Sciences, University of Bristol, Bristol, BS8 1TQ, United Kingdom
| | - John W Moreau
- School of Geographical, Atmospheric and Earth Sciences, The University of Melbourne, Parkville, Victoria 3010, Australia
- School of Geographical and Earth Sciences, University of Glasgow, Glasgow, G12 8RZ, United Kingdom
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5
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Capo E, Peterson BD, Kim M, Jones DS, Acinas SG, Amyot M, Bertilsson S, Björn E, Buck M, Cosio C, Elias DA, Gilmour C, Goñi Urriza MS, Gu B, Lin H, Liu YR, McMahon K, Moreau JW, Pinhassi J, Podar M, Puente-Sánchez F, Sánchez P, Storck V, Tada Y, Vigneron A, Walsh D, Vandewalle-Capo M, Bravo AG, Gionfriddo C. A consensus protocol for the recovery of mercury methylation genes from metagenomes. Mol Ecol Resour 2022; 23:190-204. [PMID: 35839241 PMCID: PMC10087281 DOI: 10.1111/1755-0998.13687] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2022] [Revised: 06/24/2022] [Accepted: 07/08/2022] [Indexed: 11/27/2022]
Abstract
Mercury (Hg) methylation genes (hgcAB) mediate the formation of the toxic methylmercury and have been identified from diverse 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 samples. 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 diversity (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.
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Affiliation(s)
- Eric Capo
- Department of Marine Biology and Oceanography, Institute of Marine Sciences, CSIC, Barcelona, 08003, Spain.,Department of Aquatic Sciences and Assessment, Swedish University of Agricultural Sciences, 75007, Uppsala, Sweden
| | - Benjamin D Peterson
- Department of Bacteriology, University of Wisconsin at Madison, 53706, Madison, WI, USA
| | - Minjae Kim
- Natural Resource Ecology Laboratory, Colorado State University, 80523, Fort Collins, CO, USA
| | - Daniel S Jones
- Department of Earth and Environmental Science, New Mexico Institute of Mining and Technology, 87801, Socorro, NM, USA.,National Cave and Karst Research Institute, 88220, Carlsbad, NM, USA
| | - Silvia G Acinas
- Department of Marine Biology and Oceanography, Institute of Marine Sciences, CSIC, Barcelona, 08003, Spain
| | - Marc Amyot
- Department of Biological Sciences, University of Montréal, Montréal, QC, H3C 5J9, Canada
| | - Stefan Bertilsson
- Department of Aquatic Sciences and Assessment, Swedish University of Agricultural Sciences, 75007, Uppsala, Sweden
| | - Erik Björn
- Department of Chemistry, Umeå University, 90736, Umeå, Sweden
| | - Moritz Buck
- Department of Aquatic Sciences and Assessment, Swedish University of Agricultural Sciences, 75007, Uppsala, Sweden
| | - Claudia Cosio
- University of Reims Champagne-Ardenne, 51100, Reims, France
| | | | - Cynthia Gilmour
- Smithsonian Environmental Research Center, 21037, Edgewater, MD, USA
| | | | - Baohua Gu
- Oak Ridge National Lab, 37830, Oak Ridge, TN, USA
| | - Heyu Lin
- School of Geography, Earth and Atmospheric Sciences, The University of Melbourne, 3010, Parkville, VIC, Australia
| | - Yu-Rong Liu
- College of Resources and Environment, Huazhong Agricultural University, 430070, Wuhan, China
| | - Katherine McMahon
- Department of Bacteriology, University of Wisconsin at Madison, 53706, Madison, WI, USA
| | - John W Moreau
- School of Geographical and Earth Sciences, University of Glasgow, G12 8RZ, Glasgow, UK
| | - Jarone Pinhassi
- Centre for Ecology and Evolution in Microbial Model Systems - EEMiS, Linnaeus University, 39231, Kalmar, Sweden
| | - Mircea Podar
- Oak Ridge National Lab, 37830, Oak Ridge, TN, USA
| | - Fernando Puente-Sánchez
- Department of Aquatic Sciences and Assessment, Swedish University of Agricultural Sciences, 75007, Uppsala, Sweden
| | - Pablo Sánchez
- Department of Marine Biology and Oceanography, Institute of Marine Sciences, CSIC, Barcelona, 08003, Spain
| | - Veronika Storck
- Department of Biological Sciences, University of Montréal, Montréal, QC, H3C 5J9, Canada
| | - Yuya Tada
- National Institute for Minamata Disease, Department of Environment and Public Health, Kumamoto, 867-0008, Japan
| | - Adrien Vigneron
- University of Pau et des Pays de l'Adour, E2S UPPA, CNRS, IPREM, Pau, 64000, France
| | - David Walsh
- Department of Biology, Concordia University, Montreal, Quebec H4BIR6, Canada
| | - Marine Vandewalle-Capo
- Department of Aquatic Sciences and Assessment, Swedish University of Agricultural Sciences, 75007, Uppsala, Sweden
| | - Andrea G Bravo
- Department of Marine Biology and Oceanography, Institute of Marine Sciences, CSIC, Barcelona, 08003, Spain
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6
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Lin H, Ascher DB, Myung Y, Lamborg CH, Hallam SJ, Gionfriddo CM, Holt KE, Moreau JW. Mercury methylation by metabolically versatile and cosmopolitan marine bacteria. ISME J 2021; 15:1810-1825. [PMID: 33504941 DOI: 10.1101/2020.06.03.132969] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/03/2020] [Accepted: 12/17/2020] [Indexed: 05/21/2023]
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.
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Affiliation(s)
- Heyu Lin
- School of Earth Sciences, The University of Melbourne, Parkville, VIC, 3010, Australia
| | - David B Ascher
- Structural Biology and Bioinformatics, Department of Biochemistry and Molecular Biology, Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Parkville, VIC, 3010, Australia
- Computational Biology and Clinical Informatics, Baker Heart and Diabetes Institute, PO Box 6492, Melbourne, VIC, 3004, Australia
| | - Yoochan Myung
- Structural Biology and Bioinformatics, Department of Biochemistry and Molecular Biology, Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Parkville, VIC, 3010, Australia
- Computational Biology and Clinical Informatics, Baker Heart and Diabetes Institute, PO Box 6492, Melbourne, VIC, 3004, Australia
| | - Carl H Lamborg
- Department of Ocean Sciences, University of California, Santa Cruz, CA, 95064, USA
| | - Steven J Hallam
- Department of Microbiology and Immunology, University of British Columbia, Vancouver, BC, V6T 1Z1, Canada
- Genome Science and Technology Program, University of British Columbia, Vancouver, BC, V6T 1Z4, Canada
| | - Caitlin M Gionfriddo
- Biosciences Division, Oak Ridge National Laboratory, PO Box 2008, Oak Ridge, TN, 37831, USA
- Smithsonian Environmental Research Center, Edgewater, MD, 21037, USA
| | - Kathryn E Holt
- Department of Infectious Diseases, Central Clinical School, Monash University, Monash, VIC, 3800, Australia
- Department of Infection Biology, London School of Hygiene & Tropical Medicine, London, WC1E 7HT, UK
| | - John W Moreau
- School of Earth Sciences, The University of Melbourne, Parkville, VIC, 3010, Australia.
- Currently at School of Geographical & Earth Sciences, University of Glasgow, Glasgow, G12 8QQ, UK.
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7
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Lin H, Ascher DB, Myung Y, Lamborg CH, Hallam SJ, Gionfriddo CM, Holt KE, Moreau JW. Mercury methylation by metabolically versatile and cosmopolitan marine bacteria. ISME J 2021; 15:1810-1825. [PMID: 33504941 PMCID: PMC8163782 DOI: 10.1038/s41396-020-00889-4] [Citation(s) in RCA: 45] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/03/2020] [Accepted: 12/17/2020] [Indexed: 01/30/2023]
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.
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Affiliation(s)
- Heyu Lin
- grid.1008.90000 0001 2179 088XSchool of Earth Sciences, The University of Melbourne, Parkville, VIC 3010 Australia
| | - David B. Ascher
- grid.1008.90000 0001 2179 088XStructural Biology and Bioinformatics, Department of Biochemistry and Molecular Biology, Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Parkville, VIC 3010 Australia ,grid.1051.50000 0000 9760 5620Computational Biology and Clinical Informatics, Baker Heart and Diabetes Institute, PO Box 6492, Melbourne, VIC 3004 Australia
| | - Yoochan Myung
- grid.1008.90000 0001 2179 088XStructural Biology and Bioinformatics, Department of Biochemistry and Molecular Biology, Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Parkville, VIC 3010 Australia ,grid.1051.50000 0000 9760 5620Computational Biology and Clinical Informatics, Baker Heart and Diabetes Institute, PO Box 6492, Melbourne, VIC 3004 Australia
| | - Carl H. Lamborg
- grid.205975.c0000 0001 0740 6917Department of Ocean Sciences, University of California, Santa Cruz, CA 95064 USA
| | - Steven J. Hallam
- grid.17091.3e0000 0001 2288 9830Department of Microbiology and Immunology, University of British Columbia, Vancouver, BC V6T 1Z1 Canada ,grid.17091.3e0000 0001 2288 9830Genome Science and Technology Program, University of British Columbia, Vancouver, BC V6T 1Z4 Canada
| | - Caitlin M. Gionfriddo
- grid.135519.a0000 0004 0446 2659Biosciences Division, Oak Ridge National Laboratory, PO Box 2008, Oak Ridge, TN 37831 USA ,grid.419533.90000 0000 8612 0361Present Address: Smithsonian Environmental Research Center, Edgewater, MD 21037 USA
| | - Kathryn E. Holt
- grid.1002.30000 0004 1936 7857Department of Infectious Diseases, Central Clinical School, Monash University, Monash, VIC 3800 Australia ,grid.8991.90000 0004 0425 469XDepartment of Infection Biology, London School of Hygiene & Tropical Medicine, London, WC1E 7HT UK
| | - John W. Moreau
- grid.1008.90000 0001 2179 088XSchool of Earth Sciences, The University of Melbourne, Parkville, VIC 3010 Australia ,grid.8756.c0000 0001 2193 314XPresent Address: Currently at School of Geographical & Earth Sciences, University of Glasgow, Glasgow, G12 8QQ UK
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8
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Shafiei F, Watts MP, Pajank L, Moreau JW. The effect of heavy metals on thiocyanate biodegradation by an autotrophic microbial consortium enriched from mine tailings. Appl Microbiol Biotechnol 2020; 105:417-427. [PMID: 33263791 PMCID: PMC7778618 DOI: 10.1007/s00253-020-10983-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2020] [Revised: 10/17/2020] [Accepted: 10/26/2020] [Indexed: 11/28/2022]
Abstract
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 hamper 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. Key points • 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. Supplementary Information The online version contains supplementary material available at 10.1007/s00253-020-10983-4.
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Affiliation(s)
- Farhad Shafiei
- School of Earth Sciences, The University of Melbourne, Parkville, VIC, 3010, Australia
| | - Mathew P Watts
- School of Earth Sciences, The University of Melbourne, Parkville, VIC, 3010, Australia
| | - Lukas Pajank
- School of Earth Sciences, The University of Melbourne, Parkville, VIC, 3010, Australia
| | - John W Moreau
- School of Earth Sciences, The University of Melbourne, Parkville, VIC, 3010, Australia. .,School of Geographical & Earth Sciences, University of Glasgow, Glasgow, G12 8QQ, UK.
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9
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Mu A, Thomas BC, Banfield JF, Moreau JW. Subsurface carbon monoxide oxidation capacity revealed through genome-resolved metagenomics of a carboxydotroph. Environ Microbiol Rep 2020; 12:525-533. [PMID: 32633030 DOI: 10.1111/1758-2229.12868] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/30/2020] [Accepted: 07/02/2020] [Indexed: 06/11/2023]
Abstract
Microbial communities play important roles in the biogeochemical cycling of carbon in the Earth's deep subsurface. Previously, we demonstrated changes to the microbial community structure of a deep aquifer (1.4 km) receiving 150 tons of injected supercritical CO2 (scCO2 ) in a geosequestration experiment. The observed changes support a key role in the aquifer microbiome for the thermophilic CO-utilizing anaerobe Carboxydocella, which decreased in relative abundance post-scCO2 injection. Here, we present results from more detailed metagenomic profiling of this experiment, with genome resolution of the native carboxydotrophic Carboxydocella. We demonstrate a switch in CO-oxidation potential by Carboxydocella through analysis of its carbon monoxide dehydrogenase (CODH) gene before and after the geosequestration experiment. We discuss the potential impacts of scCO2 on subsurface flow of carbon and electrons from oxidation of the metabolic intermediate carbon monoxide (CO).
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Affiliation(s)
- Andre Mu
- Department of Microbiology and Immunology, The Peter Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, Australia
- Doherty Applied Microbial Genomics, Department of Microbiology and Immunology, The Peter Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, Australia
| | - Brian C Thomas
- Department of Earth and Planetary Science, University of California, Berkeley, CA, USA
| | - Jillian F Banfield
- Department of Earth and Planetary Science, University of California, Berkeley, CA, USA
- Innovative Genomics Institute, University of California, Berkeley, CA, USA
| | - John W Moreau
- School of Earth Sciences, University of Melbourne, Melbourne, Australia
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10
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Watts MP, Spurr LP, Lê Cao KA, Wick R, Banfield JF, Moreau JW. Genome-resolved metagenomics of an autotrophic thiocyanate-remediating microbial bioreactor consortium. Water Res 2019; 158:106-117. [PMID: 31022528 DOI: 10.1016/j.watres.2019.02.058] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/06/2018] [Revised: 02/25/2019] [Accepted: 02/26/2019] [Indexed: 06/09/2023]
Abstract
Industrial thiocyanate (SCN-) waste streams from gold mining and coal coking have polluted environments worldwide. Modern SCN- bioremediation involves use of complex engineered heterotrophic microbiomes; little attention has been given to the ability of a simple environmental autotrophic microbiome to biodegrade SCN-. Here we present results from a bioreactor experiment inoculated with SCN- -loaded mine tailings, incubated autotrophically, and subjected to a range of environmentally relevant conditions. Genome-resolved metagenomics revealed that SCN- hydrolase-encoding, sulphur-oxidizing autotrophic bacteria mediated SCN- degradation. These microbes supported metabolically-dependent non-SCN--degrading sulphur-oxidizing autotrophs and non-sulphur oxidizing heterotrophs, and "niche" microbiomes developed spatially (planktonic versus sessile) and temporally (across changing environmental parameters). Bioreactor microbiome structures changed significantly with increasing temperature, shifting from Thiobacilli to a novel SCN- hydrolase-encoding gammaproteobacteria. Transformation of carbonyl sulphide (COS), a key intermediate in global biogeochemical sulphur cycling, was mediated by plasmid-hosted CS2 and COS hydrolase genes associated with Thiobacillus, revealing a potential for horizontal transfer of this function. Our work shows that simple native autotrophic microbiomes from mine tailings can be employed for SCN- bioremediation, thus improving the recycling of ore processing waters and reducing the hydrological footprint of mining.
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Affiliation(s)
- Mathew P Watts
- School of Earth Sciences, The University of Melbourne, Parkville, VIC 3010, Australia
| | - Liam P Spurr
- School of Earth Sciences, The University of Melbourne, Parkville, VIC 3010, Australia
| | - Kim-Anh Lê Cao
- Melbourne Integrative Genomics and School of Mathematics and Statistics, The University of Melbourne, Parkville, VIC 3010, Australia
| | - Ryan Wick
- Department of Biochemistry and Molecular Biology, Bio21, The University of Melbourne, Parkville, VIC 3010, Australia
| | - Jillian F Banfield
- School of Earth Sciences, The University of Melbourne, Parkville, VIC 3010, Australia; Department of Earth and Planetary Sciences, University of California, Berkeley, CA 94720, USA; Department of Environmental Science, Policy and Management, University of California, Berkeley, CA 94720, USA
| | - John W Moreau
- School of Earth Sciences, The University of Melbourne, Parkville, VIC 3010, Australia.
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11
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Spurr LP, Watts MP, Gan HM, Moreau JW. Biodegradation of thiocyanate by a native groundwater microbial consortium. PeerJ 2019; 7:e6498. [PMID: 30941266 PMCID: PMC6440457 DOI: 10.7717/peerj.6498] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2017] [Accepted: 01/20/2019] [Indexed: 02/01/2023] Open
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 NH4+ 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.
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Affiliation(s)
- Liam P Spurr
- School of Earth Sciences, University of Melbourne, Parkville, Australia
| | - Mathew P Watts
- School of Earth Sciences, University of Melbourne, Parkville, Australia
| | - Han M Gan
- School of Life and Environmental Sciences, Deakin University, Waurn Ponds, Australia
| | - John W Moreau
- School of Earth Sciences, University of Melbourne, Parkville, Australia
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12
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Cox TL, Gan HM, Moreau JW. Seawater recirculation through subducting sediments sustains a deeply buried population of sulfate-reducing bacteria. Geobiology 2019; 17:172-184. [PMID: 30474350 DOI: 10.1111/gbi.12324] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/31/2018] [Accepted: 10/10/2018] [Indexed: 06/09/2023]
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 samples. 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 diversity, potential function, and physiological tolerance of a community of sulfate-reducing bacteria living at ~480 m below subducting seafloor.
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Affiliation(s)
- Toni L Cox
- School of Earth Sciences, The University of Melbourne, Parkville, Victoria, Australia
| | - Han Ming Gan
- School of Life and Environmental Sciences, Centre for Integrative Ecology, Deakin University, Victoria, Australia
| | - John W Moreau
- School of Earth Sciences, The University of Melbourne, Parkville, Victoria, Australia
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13
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Cumberland SA, Etschmann B, Brugger J, Douglas G, Evans K, Fisher L, Kappen P, Moreau JW. Characterization of uranium redox state in organic-rich Eocene sediments. Chemosphere 2018; 194:602-613. [PMID: 29241135 DOI: 10.1016/j.chemosphere.2017.12.012] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/27/2017] [Revised: 11/29/2017] [Accepted: 12/03/2017] [Indexed: 06/07/2023]
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 samples), plus a lignite sample from the Mulga Rock polymetallic deposit in Western Australia. Uranium was unevenly dispersed within the analysed samples with 84% of the total U occurring in samples 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.
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Affiliation(s)
- Susan A Cumberland
- School of Earth Sciences, University of Melbourne, Parkville, Victoria 3100, Australia; School of Earth, Atmosphere and Environment, Monash University, Clayton 3800, Victoria, Australia; ANSTO Australian Synchrotron, 800 Blackburn Road, Clayton 3168, Victoria, Australia.
| | - Barbara Etschmann
- School of Earth, Atmosphere and Environment, Monash University, Clayton 3800, Victoria, Australia
| | - Joël Brugger
- School of Earth, Atmosphere and Environment, Monash University, Clayton 3800, Victoria, Australia
| | - Grant Douglas
- CSIRO Land and Water, Floreat, Western Australia, Australia
| | - Katy Evans
- Western Australian School of Mines, Curtin University, Bentley, Western Australia, Australia
| | - Louise Fisher
- CSIRO Mineral Resources, Bentley, Western Australia, Australia
| | - Peter Kappen
- ANSTO Australian Synchrotron, 800 Blackburn Road, Clayton 3168, Victoria, Australia
| | - John W Moreau
- School of Earth Sciences, University of Melbourne, Parkville, Victoria 3100, Australia.
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14
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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.
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15
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Watts MP, Gan HM, Peng LY, Lê Cao KA, Moreau JW. In Situ Stimulation of Thiocyanate Biodegradation through Phosphate Amendment in Gold Mine Tailings Water. Environ Sci Technol 2017; 51:13353-13362. [PMID: 29064247 DOI: 10.1021/acs.est.7b04152] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Thiocyanate (SCN-) is a contaminant requiring remediation in gold mine tailings and wastewaters globally. Seepage of SCN--contaminated waters into aquifers can occur from unlined or structurally compromised mine tailings storage facilities. A wide variety of microorganisms are known to be capable of biodegrading SCN-; however, little is known regarding the potential of native microbes for in situ SCN- biodegradation, a remediation option that is less costly than engineered approaches. Here we experimentally characterize the principal biogeochemical barrier to SCN- biodegradation for an autotrophic microbial consortium enriched from mine tailings, to arrive at an environmentally realistic assessment of in situ SCN- biodegradation potential. Upon amendment with phosphate, the consortium completely degraded up to ∼10 mM SCN- to ammonium and sulfate, with some evidence of nitrification of the ammonium to nitrate. Although similarly enriched in known SCN--degrading strains of thiobacilli, this consortium differed in its source (mine tailings) and metabolism (autotrophy) from those of previous studies. Our results provide a proof of concept that phosphate limitation may be the principal barrier to in situ SCN- biodegradation in mine tailing waters and also yield new insights into the microbial ecology of in situ SCN- bioremediation involving autotrophic sulfur-oxidizing bacteria.
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Affiliation(s)
- Mathew P Watts
- School of Earth Sciences, The University of Melbourne , Parkville, Victoria, Australia
| | - Han M Gan
- Centre for Integrative Ecology, School of Life and Environmental Sciences, Deakin University , Geelong, Victoria, Australia
- School of Science, Monash University Malaysia , Bandar Sunway, Petaling Jaya, Selangor, Malaysia
- Genomics Facility, Tropical Medicine and Biology Platform, Monash University Malaysia , Bandar Sunway, Petaling Jaya, Selangor, Malaysia
| | - Lee Y Peng
- School of Science, Monash University Malaysia , Bandar Sunway, Petaling Jaya, Selangor, Malaysia
- Genomics Facility, Tropical Medicine and Biology Platform, Monash University Malaysia , Bandar Sunway, Petaling Jaya, Selangor, Malaysia
| | - Kim-Anh Lê Cao
- Melbourne Integrative Genomics and the School of Mathematics and Statistics, The University of Melbourne , Parkville, Victoria, Australia
| | - John W Moreau
- School of Earth Sciences, The University of Melbourne , Parkville, Victoria, Australia
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16
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Hug K, Maher WA, Foster S, Krikowa F, Moreau JW. Experimental evaluation of sampling, storage and analytical protocols for measuring arsenic speciation in sulphidic hot spring waters. Microchem J 2017. [DOI: 10.1016/j.microc.2016.08.008] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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17
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Gionfriddo CM, Tate MT, Wick RR, Schultz MB, Zemla A, Thelen MP, Schofield R, Krabbenhoft DP, Holt KE, Moreau JW. Microbial mercury methylation in Antarctic sea ice. Nat Microbiol 2016; 1:16127. [PMID: 27670112 DOI: 10.1038/nmicrobiol.2016.127] [Citation(s) in RCA: 101] [Impact Index Per Article: 12.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2015] [Accepted: 06/29/2016] [Indexed: 11/09/2022]
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.
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Affiliation(s)
- Caitlin M Gionfriddo
- School of Earth Sciences, University of Melbourne, Parkville, Victoria 3010, Australia
| | - Michael T Tate
- Wisconsin Water Science Center, US Geological Survey, Middleton, Wisconsin 53562, USA
| | - Ryan R Wick
- Centre for Systems Genomics, University of Melbourne, Victoria 3010, Australia.,Department of Biochemistry and Molecular Biology, Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Victoria 3010, Australia
| | - Mark B Schultz
- Centre for Systems Genomics, University of Melbourne, Victoria 3010, Australia.,Department of Biochemistry and Molecular Biology, Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Victoria 3010, Australia
| | - Adam Zemla
- Computation Directorate, Lawrence Livermore National Laboratory, Livermore, California 94550 USA
| | - Michael P Thelen
- Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, California 94550, USA
| | - Robyn Schofield
- School of Earth Sciences, University of Melbourne, Parkville, Victoria 3010, Australia
| | - David P Krabbenhoft
- Wisconsin Water Science Center, US Geological Survey, Middleton, Wisconsin 53562, USA
| | - Kathryn E Holt
- Centre for Systems Genomics, University of Melbourne, Victoria 3010, Australia.,Department of Biochemistry and Molecular Biology, Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Victoria 3010, Australia
| | - John W Moreau
- School of Earth Sciences, University of Melbourne, Parkville, Victoria 3010, Australia
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18
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Moreau JW, Gionfriddo CM, Krabbenhoft DP, Ogorek JM, DeWild JF, Aiken GR, Roden EE. The Effect of Natural Organic Matter on Mercury Methylation by Desulfobulbus propionicus 1pr3. Front Microbiol 2015; 6:1389. [PMID: 26733947 PMCID: PMC4683176 DOI: 10.3389/fmicb.2015.01389] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2015] [Accepted: 11/23/2015] [Indexed: 11/13/2022] Open
Abstract
Methylation of tracer and ambient mercury ((200)Hg and (202)Hg, respectively) equilibrated with four different natural organic matter (NOM) isolates was investigated in vivo using the Hg-methylating sulfate-reducing bacterium Desulfobulbus propionicus 1pr3. Desulfobulbus cultures grown fermentatively with environmentally representative concentrations of dissolved NOM isolates, Hg[II], and HS(-) were assayed for absolute methylmercury (MeHg) concentration and conversion of Hg(II) to MeHg relative to total unfiltered Hg(II). Results showed the (200)Hg tracer was methylated more efficiently in the presence of hydrophobic NOM isolates than in the presence of transphilic NOM, or in the absence of NOM. Different NOM isolates were associated with variable methylation efficiencies for either the (202)Hg tracer or ambient (200)Hg. One hydrophobic NOM, F1 HpoA derived from dissolved organic matter from the Florida Everglades, was equilibrated for different times with Hg tracer, which resulted in different methylation rates. A 5 day equilibration with F1 HpoA resulted in more MeHg production than either the 4 h or 30 day equilibration periods, suggesting a time dependence for NOM-enhanced Hg bioavailability for methylation.
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Affiliation(s)
- John W Moreau
- School of Earth Sciences, University of Melbourne Melbourne, VIC, Australia
| | | | | | | | | | | | - Eric E Roden
- Department of Geology and Geophysics, University of Wisconsin-Madison Madison, WI, USA
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19
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Torres ME, Cox T, Hong WL, McManus J, Sample JC, Destrigneville C, Gan HM, Gan HY, Moreau JW. Crustal fluid and ash alteration impacts on the biosphere of Shikoku Basin sediments, Nankai Trough, Japan. Geobiology 2015; 13:562-580. [PMID: 26081483 DOI: 10.1111/gbi.12146] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/01/2014] [Accepted: 05/09/2015] [Indexed: 06/04/2023]
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 samples 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.
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Affiliation(s)
- M E Torres
- CEOAS, Oregon State University, Corvallis, OR, USA
| | - T Cox
- School of Earth Sciences, University of Melbourne, Parkville, Vic., Australia
| | - W-L Hong
- CEOAS, Oregon State University, Corvallis, OR, USA
| | - J McManus
- CEOAS, Oregon State University, Corvallis, OR, USA
- Department of Geosciences, University of Akron, Akron, OH, USA
| | - J C Sample
- School of Earth Sciences & Environmental Sustainability, Northern Arizona University, Flagstaff, AZ, USA
| | | | - H M Gan
- School of Science, Monash University Malaysia, Jalan Lagoon Selatan, Bandar Sunway, Petaling Jaya, Selangor, Malaysia
| | - H Y Gan
- School of Science, Monash University Malaysia, Jalan Lagoon Selatan, Bandar Sunway, Petaling Jaya, Selangor, Malaysia
| | - J W Moreau
- School of Earth Sciences, University of Melbourne, Parkville, Vic., Australia
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20
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Houghton KM, Morgan XC, Lagutin K, MacKenzie AD, Vyssotskii M, Mitchell KA, McDonald IR, Morgan HW, Power JF, Moreau JW, Hanssen E, Stott MB. Thermorudis pharmacophila sp. nov., a novel member of the class Thermomicrobia isolated from geothermal soil, and emended descriptions of Thermomicrobium roseum, Thermomicrobium carboxidum, Thermorudis peleae and Sphaerobacter thermophilus. Int J Syst Evol Microbiol 2015; 65:4479-4487. [PMID: 26374291 DOI: 10.1099/ijsem.0.000598] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
An aerobic, thermophilic and cellulolytic bacterium, designated strain WKT50.2T, was isolated from geothermal soil at Waikite, New Zealand. Strain WKT50.2T 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 C18 : 0 and C18 : 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 WKT50.2T utilized a range of cellulosic substrates, alcohols and organic acids for growth, but was unable to utilize monosaccharides. Robust growth of WKT50.2T was observed on protein derivatives. WKT50.2T was sensitive to ampicillin, chloramphenicol, kanamycin, neomycin, polymyxin B, streptomycin and vancomycin. Metronidazole, lasalocid A and trimethoprim stimulated growth. Phylogenetic analysis of 16S rRNA gene sequences showed that WKT50.2T belonged to the class Thermomicrobia within the phylum Chloroflexi, and was most closely related to Thermorudis peleae KI4T (99.6% similarity). DNA-DNA hybridization between WKT50.2T and Thermorudis peleae DSM 27169T was 18.0%. Physiological and biochemical tests confirmed the phenotypic and genotypic differentiation of strain WKT50.2T from Thermorudis peleae KI4T and other members of the Thermomicrobia. On the basis of its phylogenetic position and phenotypic characteristics, we propose that strain WKT50.2T represents a novel species, for which the name Thermorudis pharmacophila sp. nov. is proposed, with the type strain WKT50.2T ( = DSM 26011T = ICMP 20042T). 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.
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Affiliation(s)
- Karen M Houghton
- GNS Science, Extremophiles Research Group, Private Bag 2000, Taupo¯ 3352, New Zealand.,School of Science, University of Waikato, Private Bag 3105, Hamilton 3240, New Zealand
| | - Xochitl C Morgan
- Department of Biostatistics, Harvard T. H. Chan School of Public Health, 655 Huntington Ave, Boston, MA 02115, USA
| | - Kirill Lagutin
- Callaghan Innovation, PO Box 31310, Lower Hutt 5040, New Zealand
| | | | | | - Kevin A Mitchell
- Callaghan Innovation, PO Box 31310, Lower Hutt 5040, New Zealand
| | - Ian R McDonald
- School of Science, University of Waikato, Private Bag 3105, Hamilton 3240, New Zealand
| | - Hugh W Morgan
- School of Science, University of Waikato, Private Bag 3105, Hamilton 3240, New Zealand
| | - Jean F Power
- GNS Science, Extremophiles Research Group, Private Bag 2000, Taupo¯ 3352, New Zealand
| | - John W Moreau
- University of Melbourne, 30 Flemington Road, Victoria 3010, Australia
| | - Eric Hanssen
- University of Melbourne, 30 Flemington Road, Victoria 3010, Australia
| | - Matthew B Stott
- GNS Science, Extremophiles Research Group, Private Bag 2000, Taupo¯ 3352, New Zealand
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21
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Ling YC, Bush R, Grice K, Tulipani S, Berwick L, Moreau JW. Distribution of iron- and sulfate-reducing bacteria across a coastal acid sulfate soil (CASS) environment: implications for passive bioremediation by tidal inundation. Front Microbiol 2015; 6:624. [PMID: 26191042 PMCID: PMC4490247 DOI: 10.3389/fmicb.2015.00624] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2014] [Accepted: 06/08/2015] [Indexed: 11/13/2022] Open
Abstract
Coastal acid sulfate soils (CASS) constitute a serious and global environmental problem. Oxidation of iron sulfide minerals exposed to air generates sulfuric acid with consequently negative impacts on coastal and estuarine ecosystems. Tidal inundation represents one current treatment strategy for CASS, with the aim of neutralizing acidity by triggering microbial iron- and sulfate-reduction and inducing the precipitation of iron-sulfides. Although well-known functional guilds of bacteria drive these processes, their distributions within CASS environments, as well as their relationships to tidal cycling and the availability of nutrients and electron acceptors, are poorly understood. These factors will determine the long-term efficacy of "passive" CASS remediation strategies. Here we studied microbial community structure and functional guild distribution in sediment cores obtained from 10 depths ranging from 0 to 20 cm in three sites located in the supra-, inter- and sub-tidal segments, respectively, of a CASS-affected salt marsh (East Trinity, Cairns, Australia). Whole community 16S rRNA gene diversity within each site was assessed by 454 pyrotag sequencing and bioinformatic analyses in the context of local hydrological, geochemical, and lithological factors. The results illustrate spatial overlap, or close association, of iron-, and sulfate-reducing bacteria (SRB) in an environment rich in organic matter and controlled by parameters such as acidity, redox potential, degree of water saturation, and mineralization. The observed spatial distribution implies the need for empirical understanding of the timing, relative to tidal cycling, of various terminal electron-accepting processes that control acid generation and biogeochemical iron and sulfur cycling.
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Affiliation(s)
- Yu-Chen Ling
- School of Earth Sciences, University of MelbourneMelbourne, VIC, Australia
| | - Richard Bush
- Southern Cross GeoScience, Southern Cross UniversityLismore, NSW, Australia
| | - Kliti Grice
- Department of Chemistry, Western Australia Organic and Isotope Geochemistry Centre, The Institute for Geoscience Research, Curtin UniversityPerth, WA, Australia
| | - Svenja Tulipani
- Department of Chemistry, Western Australia Organic and Isotope Geochemistry Centre, The Institute for Geoscience Research, Curtin UniversityPerth, WA, Australia
| | - Lyndon Berwick
- Department of Chemistry, Western Australia Organic and Isotope Geochemistry Centre, The Institute for Geoscience Research, Curtin UniversityPerth, WA, Australia
| | - John W. Moreau
- School of Earth Sciences, University of MelbourneMelbourne, VIC, Australia
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Mu A, Moreau JW. The geomicrobiology of CO2 geosequestration: a focused review on prokaryotic community responses to field-scale CO2 injection. Front Microbiol 2015; 6:263. [PMID: 25914677 PMCID: PMC4391042 DOI: 10.3389/fmicb.2015.00263] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2014] [Accepted: 03/16/2015] [Indexed: 11/13/2022] Open
Abstract
Our primary research paper (Mu et al., 2014) demonstrated selective changes to a deep subsurface prokaryotic community as a result of CO2 stress. Analyzing geochemical and microbial 16S rRNA gene profiles, we evaluated how in situ prokaryotic communities responded to increased CO2 and the presence of trace organic compounds, and related temporal shifts in phylogeny to changes in metabolic potential. In this focused review, we extend upon our previous discussion to present analysis of taxonomic unit co-occurrence profiles from the same field experiment, to attempt to describe dynamic community behavior within the deep subsurface. Understanding the physiology of the subsurface microbial biosphere, including how key functional groups integrate into the community, will be critical to determining the fate of injected CO2. For example, community-wide network analyses may provide insights to whether microbes cooperatively produce biofilm biomass, and/or biomineralize the CO2, and hence, induce changes to formation porosity or changes in electron flow. Furthermore, we discuss potential impacts to the feasibility of subsurface CO2 storage of selectively enriching for particular metabolic functions (e.g., methanogenesis) as a result of CO2 injection.
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Affiliation(s)
- Andre Mu
- Moreau Lab, School of Earth Sciences, Faculty of Science, University of Melbourne Melbourne, VIC, Australia ; Department of Microbiology and Immunology, Peter Doherty Institute for Infection and Immunity, University of Melbourne Melbourne, VIC, Australia
| | - John W Moreau
- Moreau Lab, School of Earth Sciences, Faculty of Science, University of Melbourne Melbourne, VIC, Australia
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23
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Anders H, Power JF, MacKenzie AD, Lagutin K, Vyssotski M, Hanssen E, Moreau JW, Stott MB. Limisphaera ngatamarikiensis gen. nov., sp. nov., a thermophilic, pink-pigmented coccus isolated from subaqueous mud of a geothermal hotspring. Int J Syst Evol Microbiol 2015; 65:1114-1121. [DOI: 10.1099/ijs.0.000063] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A novel bacterial strain, NGM72.4T, 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). NGM72.4T 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 (>15 %) were C16 : 0, anteiso-C15 : 0, iso-C16 : 0 and anteiso-C17 : 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. NGM72.4T 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 NGM72.4T 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 NGM72.4T ( = ICMP 20182T = DSM 27329T).
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Affiliation(s)
- Heike Anders
- Lehrstuhl für Tierhygiene, Technische Universität München, Weihenstephaner Berg 3 0D-85354, Freising, Germany
- GNS Science, Extremophile Research Group, Private Bag 2000, Taupō 3352, New Zealand
| | - Jean F. Power
- GNS Science, Extremophile Research Group, Private Bag 2000, Taupō 3352, New Zealand
| | | | - Kirill Lagutin
- Callaghan Innovation, PO Box 31310, Lower Hutt 5040, New Zealand
| | | | - Eric Hanssen
- University of Melbourne, 30 Flemington Road, Victoria 3010, Australia
| | - John W. Moreau
- University of Melbourne, 30 Flemington Road, Victoria 3010, Australia
| | - Matthew B. Stott
- GNS Science, Extremophile Research Group, Private Bag 2000, Taupō 3352, New Zealand
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24
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Vu HP, Moreau JW. Thiocyanate adsorption on ferrihydrite and its fate during ferrihydrite transformation to hematite and goethite. Chemosphere 2015; 119:987-993. [PMID: 25303658 DOI: 10.1016/j.chemosphere.2014.09.019] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/10/2014] [Revised: 09/04/2014] [Accepted: 09/05/2014] [Indexed: 06/04/2023]
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.
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Affiliation(s)
- Hong Phuc Vu
- School of Earth Sciences, University of Melbourne, Victoria 3010, Australia.
| | - John W Moreau
- School of Earth Sciences, University of Melbourne, Victoria 3010, Australia
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25
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Hug K, Maher WA, Stott MB, Krikowa F, Foster S, Moreau JW. Microbial contributions to coupled arsenic and sulfur cycling in the acid-sulfide hot spring Champagne Pool, New Zealand. Front Microbiol 2014; 5:569. [PMID: 25414696 PMCID: PMC4220137 DOI: 10.3389/fmicb.2014.00569] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2014] [Accepted: 10/09/2014] [Indexed: 11/13/2022] Open
Abstract
Acid-sulfide hot springs are analogs of early Earth geothermal systems where microbial metal(loid) resistance likely first evolved. Arsenic is a metalloid enriched in the acid-sulfide hot spring Champagne Pool (Waiotapu, New Zealand). Arsenic speciation in Champagne Pool follows reaction paths not yet fully understood with respect to biotic contributions and coupling to biogeochemical sulfur cycling. Here we present quantitative arsenic speciation from Champagne Pool, finding arsenite dominant in the pool, rim and outflow channel (55-75% total arsenic), and dithio- and trithioarsenates ubiquitously present as 18-25% total arsenic. In the outflow channel, dimethylmonothioarsenate comprised ≤9% total arsenic, while on the outflow terrace thioarsenates were present at 55% total arsenic. We also quantified sulfide, thiosulfate, sulfate and elemental sulfur, finding sulfide and sulfate as major species in the pool and outflow terrace, respectively. Elemental sulfur concentration reached a maximum at the terrace. Phylogenetic analysis of 16S rRNA genes from metagenomic sequencing revealed the dominance of Sulfurihydrogenibium at all sites and an increased archaeal population at the rim and outflow channel. Several phylotypes were found closely related to known sulfur- and sulfide-oxidizers, as well as sulfur- and sulfate-reducers. Bioinformatic analysis revealed genes underpinning sulfur redox transformations, consistent with sulfur speciation data, and illustrating a microbial role in sulfur-dependent transformation of arsenite to thioarsenate. Metagenomic analysis also revealed genes encoding for arsenate reductase at all sites, reflecting the ubiquity of thioarsenate and a need for microbial arsenate resistance despite anoxic conditions. Absence of the arsenite oxidase gene, aio, at all sites suggests prioritization of arsenite detoxification over coupling to energy conservation. Finally, detection of methyl arsenic in the outflow channel, in conjunction with increased sequences from Aquificaceae, supports a role for methyltransferase in thermophilic arsenic resistance. Our study highlights microbial contributions to coupled arsenic and sulfur cycling at Champagne Pool, with implications for understanding the evolution of microbial arsenic resistance in sulfidic geothermal systems.
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Affiliation(s)
- Katrin Hug
- Geomicrobiology Laboratory, School of Earth Sciences, University of MelbourneMelbourne, VIC, Australia
| | - William A. Maher
- Ecochemistry Laboratory, Institute for Applied Ecology, University of CanberraCanberra, ACT, Australia
| | | | - Frank Krikowa
- Ecochemistry Laboratory, Institute for Applied Ecology, University of CanberraCanberra, ACT, Australia
| | - Simon Foster
- Ecochemistry Laboratory, Institute for Applied Ecology, University of CanberraCanberra, ACT, Australia
| | - John W. Moreau
- Geomicrobiology Laboratory, School of Earth Sciences, University of MelbourneMelbourne, VIC, Australia
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26
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Mu A, Boreham C, Leong HX, Haese RR, Moreau JW. Changes in the deep subsurface microbial biosphere resulting from a field-scale CO2 geosequestration experiment. Front Microbiol 2014; 5:209. [PMID: 24860559 PMCID: PMC4030138 DOI: 10.3389/fmicb.2014.00209] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2014] [Accepted: 04/19/2014] [Indexed: 01/08/2023] Open
Abstract
Subsurface microorganisms may respond to increased CO2 levels in ways that significantly affect pore fluid chemistry. Changes in CO2 concentration or speciation may result from the injection of supercritical CO2 (scCO2) into deep aquifers. Therefore, understanding subsurface microbial responses to scCO2, or unnaturally high levels of dissolved CO2, will help to evaluate the use of geosequestration to reduce atmospheric CO2 emissions. This study characterized microbial community changes at the 16S rRNA gene level during a scCO2 geosequestration experiment in the 1.4 km-deep Paaratte Formation of the Otway Basin, Australia. One hundred and fifty tons of mixed scCO2 and groundwater was pumped into the sandstone Paaratte aquifer over 4 days. A novel U-tube sampling system was used to obtain groundwater samples under in situ pressure conditions for geochemical analyses and DNA extraction. Decreases in pH and temperature of 2.6 log units and 5.8°C, respectively, were observed. Polyethylene glycols (PEGs) were detected in the groundwater prior to scCO2 injection and were interpreted as residual from drilling fluid used during the emplacement of the CO2 injection well. Changes in microbial community structure prior to scCO2 injection revealed a general shift from Firmicutes to Proteobacteria concurrent with the disappearance of PEGs. However, the scCO2 injection event, including changes in response to the associated variables (e.g., pH, temperature and salinity), resulted in increases in the relative abundances of Comamonadaceae and Sphingomonadaceae suggesting the potential for enhanced scCO2 tolerance of these groups. This study demonstrates a successful new in situ sampling approach for detecting microbial community changes associated with an scCO2 geosequestration event.
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Affiliation(s)
- Andre Mu
- School of Earth Sciences, Faculty of Science, University of Melbourne Melbourne, VIC, Australia ; Department of Microbiology and Immunology, University of Melbourne, Peter Doherty Institute for Infection and Immunity Melbourne, VIC, Australia ; Cooperative Research Centre for Greenhouse Gas Technologies Canberra, NSW, Australia
| | - Chris Boreham
- Cooperative Research Centre for Greenhouse Gas Technologies Canberra, NSW, Australia ; Geoscience Australia Canberra, NSW, Australia
| | - Henrietta X Leong
- School of Earth Sciences, Faculty of Science, University of Melbourne Melbourne, VIC, Australia ; Cooperative Research Centre for Greenhouse Gas Technologies Canberra, NSW, Australia
| | - Ralf R Haese
- School of Earth Sciences, Faculty of Science, University of Melbourne Melbourne, VIC, Australia ; Cooperative Research Centre for Greenhouse Gas Technologies Canberra, NSW, Australia
| | - John W Moreau
- School of Earth Sciences, Faculty of Science, University of Melbourne Melbourne, VIC, Australia ; Cooperative Research Centre for Greenhouse Gas Technologies Canberra, NSW, Australia
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27
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Anders H, Dunfield PF, Lagutin K, Houghton KM, Power JF, MacKenzie AD, Vyssotski M, Ryan JLJ, Hanssen EG, Moreau JW, Stott MB. Thermoflavifilum aggregans gen. nov., sp. nov., a thermophilic and slightly halophilic filamentous bacterium from the phylum Bacteroidetes. Int J Syst Evol Microbiol 2014; 64:1264-1270. [PMID: 24425740 DOI: 10.1099/ijs.0.057463-0] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
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)).
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Affiliation(s)
- Heike Anders
- Lehrstuhl für Tierhygiene, Technische Universität München, Weihenstephaner Berg 3 0D-85354, Freising, Germany
- GNS Science, Extremophile Research Group, Private Bag 2000, Taupo 3352, New Zealand
| | - Peter F Dunfield
- Department of Biological Sciences, University of Calgary, 2500 University Dr. NW, Calgary T2N 1N4, Canada
| | - Kirill Lagutin
- Callaghan Innovation, PO Box 31310, Lower Hutt 5040, New Zealand
| | - Karen M Houghton
- GNS Science, Extremophile Research Group, Private Bag 2000, Taupo 3352, New Zealand
| | - Jean F Power
- GNS Science, Extremophile Research Group, Private Bag 2000, Taupo 3352, New Zealand
| | | | | | - Jason L J Ryan
- Callaghan Innovation, PO Box 31310, Lower Hutt 5040, New Zealand
| | - Eric G Hanssen
- University of Melbourne, 30 Flemington Road, Victoria 3010, Australia
| | - John W Moreau
- University of Melbourne, 30 Flemington Road, Victoria 3010, Australia
| | - Matthew B Stott
- GNS Science, Extremophile Research Group, Private Bag 2000, Taupo 3352, New Zealand
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Moreau JW, Fournelle JH, Banfield JF. Quantifying heavy metals sequestration by sulfate-reducing bacteria in an Acid mine drainage-contaminated natural wetland. Front Microbiol 2013; 4:43. [PMID: 23487496 PMCID: PMC3594707 DOI: 10.3389/fmicb.2013.00043] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2013] [Accepted: 02/18/2013] [Indexed: 11/17/2022] Open
Abstract
Bioremediation strategies that depend on bacterial sulfate reduction for heavy metals remediation harness the reactivity of these metals with biogenic aqueous sulfide. Quantitative knowledge of the degree to which specific toxic metals are partitioned into various sulfide, oxide, or other phases is important for predicting the long-term mobility of these metals under environmental conditions. Here we report the quantitative partitioning into sedimentary biogenic sulfides of a suite of metals and metalloids associated with acid mine drainage contamination of a natural estuarine wetland for over a century.
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Affiliation(s)
- John W Moreau
- School of Earth Sciences, University of Melbourne Parkville, VIC, Australia
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29
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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 example 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.
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Affiliation(s)
- John W Moreau
- Department of Earth and Planetary Science, University of California Berkeley, Berkeley, CA 94720, USA.
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30
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Moreau JW, Sharp TG. A transmission electron microscopy study of silica and kerogen biosignatures in approximately 1.9 Ga gunflint microfossils. Astrobiology 2004; 4:196-210. [PMID: 15253838 DOI: 10.1089/153110704323175142] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
Microfossils preserved in chert from the;1.9 Ga Gunflint Formation (Schreiber Beach, Ontario, Canada) were studied with transmission electron microscopy (TEM) and analytical TEM (ATEM). Our goals were to uncover the style of silicification relative to the distribution of organic matter, and to evaluate the distribution and evolution of organic matter, at submicroscopic spatial scales. Petrographically the microfossils typically display filamentous or coccoidal morphologies, and consist of quartz crystals surrounded by kerogen along grain boundaries. ATEM analysis revealed that quartz associated with kerogen consists of 200-500nm-sized, round crystallites, whereas the chert matrix is comprised of randomly oriented, polygonal microquartz (5-10 microm). Silica spheroids found within some fossils consist of quartz subgrains in an amorphous to poorly crystalline matrix, suggesting that precipitation of opaline silica on organic matter occurred with subsequent but incomplete transformation to quartz. Some coccoidal microfossils surround large euhedral quartz crystals (up to 5 microm in diameter) that appeared to have influenced the distribution of kerogen during crystal growth. These euhedral quartz crystals commonly contain elongated (50-100 nm) iron-rich crystallites. Energy-loss, near-edge structure analysis of kerogen associated with a coccoidal microfossil showed that it is composed of amorphous carbon with no evidence of graphitization. TEM results revealed significant differences in the style of silicification between microbe-shaped microfossils and their surrounding chert matrix, as well as the presence of amorphous kerogen.
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Affiliation(s)
- John W Moreau
- Department of Geological Sciences, Arizona State University, Tempe, Arizona 85287-1404, USA
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Abstract
If life ever existed, or still exists, on Mars, its record is likely to be found in minerals formed by, or in association with, microorganisms. An important concept regarding interpretation of the mineralogical record for evidence of life is that, broadly defined, life perturbs disequilibria that arise due to kinetic barriers and can impart unexpected structure to an abiotic system. Many features of minerals and mineral assemblages may serve as biosignatures even if life does not have a familiar terrestrial chemical basis. Biological impacts on minerals and mineral assemblages may be direct or indirect. Crystalline or amorphous biominerals, an important category of mineralogical biosignatures, precipitate under direct cellular control as part of the life cycle of the organism (shells, tests, phytoliths) or indirectly when cell surface layers provide sites for heterogeneous nucleation. Biominerals also form indirectly as by-products of metabolism due to changing mineral solubility. Mineralogical biosignatures include distinctive mineral surface structures or chemistry that arise when dissolution and/or crystal growth kinetics are influenced by metabolic by-products. Mineral assemblages themselves may be diagnostic of the prior activity of organisms where barriers to precipitation or dissolution of specific phases have been overcome. Critical to resolving the question of whether life exists, or existed, on Mars is knowing how to distinguish biologically induced structure and organization patterns from inorganic phenomena and inorganic self-organization. This task assumes special significance when it is acknowledged that the majority of, and perhaps the only, material to be returned from Mars will be mineralogical.
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Affiliation(s)
- J F Banfield
- Department of Geology and Geophysics, University of Wisconsin, Madison, WI, USA.
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