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Tejedor‐Sanz S, Song YE, Sundstrom ER. Utilization of formic acid by extremely thermoacidophilic archaea species. Microb Biotechnol 2024; 17:e70003. [PMID: 39215388 PMCID: PMC11364514 DOI: 10.1111/1751-7915.70003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2024] [Accepted: 08/06/2024] [Indexed: 09/04/2024] Open
Abstract
The exploration of novel hosts with the ability to assimilate formic acid, a C1 substrate that can be produced from renewable electrons and CO2, is of great relevance for developing novel and sustainable biomanufacturing platforms. Formatotrophs can use formic acid or formate as a carbon and/or reducing power source. Formatotrophy has typically been studied in neutrophilic microorganisms because formic acid toxicity increases in acidic environments below the pKa of 3.75 (25°C). Because of this toxicity challenge, utilization of formic acid as either a carbon or energy source has been largely unexplored in thermoacidophiles, species that possess the ability to produce a variety of metabolites and enzymes of high biotechnological relevance. Here we investigate the capacity of several thermoacidophilic archaea species from the Sulfolobales order to tolerate and metabolize formic acid. Metallosphaera prunae, Sulfolobus metallicus and Sulfolobus acidocaldarium were found to metabolize and grow with 1-2 mM of formic acid in batch cultivations. Formic acid was co-utilized by this species alongside physiological electron donors, including ferrous iron. To enhance formic acid utilization while maintaining aqueous concentrations below the toxicity threshold, we developed a bioreactor culturing method based on a sequential formic acid feeding strategy. By dosing small amounts of formic acid sequentially and feeding H2 as co-substrate, M. prunae could utilize a total of 16.3 mM of formic acid and grow to higher cell densities than when H2 was supplied as a sole electron donor. These results demonstrate the viability of culturing thermoacidophilic species with formic acid as an auxiliary substrate in bioreactors to obtain higher cell densities than those yielded by conventional autotrophic conditions. Our work underscores the significance of formic acid metabolism in extreme habitats and holds promise for biotechnological applications in the realm of sustainable energy production and environmental remediation.
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Affiliation(s)
- Sara Tejedor‐Sanz
- Lawrence Berkeley National LaboratoryBerkeleyCaliforniaUSA
- Advanced Biofuel and Bioproducts Process Development Unit, Lawrence Berkeley National LaboratoryEmeryvilleCaliforniaUSA
| | - Young Eun Song
- Lawrence Berkeley National LaboratoryBerkeleyCaliforniaUSA
- Advanced Biofuel and Bioproducts Process Development Unit, Lawrence Berkeley National LaboratoryEmeryvilleCaliforniaUSA
| | - Eric R. Sundstrom
- Lawrence Berkeley National LaboratoryBerkeleyCaliforniaUSA
- Advanced Biofuel and Bioproducts Process Development Unit, Lawrence Berkeley National LaboratoryEmeryvilleCaliforniaUSA
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2
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Manesh MJH, Willard DJ, John KM, Kelly RM. Chalcopyrite bioleaching efficacy by extremely thermoacidophilic archaea leverages balanced iron and sulfur biooxidation. BIORESOURCE TECHNOLOGY 2024; 408:131198. [PMID: 39097239 DOI: 10.1016/j.biortech.2024.131198] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/14/2024] [Revised: 07/09/2024] [Accepted: 07/31/2024] [Indexed: 08/05/2024]
Abstract
Factors that contribute to optimal chalcopyrite bioleaching by extremely thermoacidophilic archaea were examined for ten species belonging to the order Sulfolobales from the genera Acidianus (A. brierleyi), Metallosphaera (M. hakonensis, M. sedula, M. prunae), Sulfuracidifex (S. metallicus, S. tepriarius), Sulfolobus (S. acidocaldarius), Saccharlobus (S. solfataricus) and Sulfurisphaera (S. ohwakuensis, S. tokodaii). Only A. brierleyi, M. sedula, S. metallicus, S. tepriarius, S. ohwakuensis, and S. tokodai exhibited significant amounts of bioleaching and were investigated further. At 70-75 °C, Chalcopyrite loadings of 10 g/l were leached for 21 days during which pH, redox potential, planktonic cell density, iron concentrations and sulfate levels were monitored, in addition to copper mobilization. S. ohwakuensis proved to be the most prolific bioleacher. This was attributed to balanced iron and sulfur oxidation, thereby reducing by-product (e.g., jarosites) formation and minimizing surface passivation. Comparative genomics suggest markers for bioleaching potential, but the results here point to the need for experimental verification.
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Affiliation(s)
- Mohamad J H Manesh
- Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, NC 27695-7905, USA
| | - Daniel J Willard
- Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, NC 27695-7905, USA
| | - Kaitlyn M John
- Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, NC 27695-7905, USA
| | - Robert M Kelly
- Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, NC 27695-7905, USA.
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3
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Willard DJ, H. Manesh MJ, Bing RG, Alexander BH, Kelly RM. Phenotype-driven assessment of the ancestral trajectory of sulfur biooxidation in the thermoacidophilic archaea Sulfolobaceae. mBio 2024; 15:e0103324. [PMID: 38953360 PMCID: PMC11323534 DOI: 10.1128/mbio.01033-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2024] [Accepted: 06/06/2024] [Indexed: 07/04/2024] Open
Abstract
Certain members of the family Sulfolobaceae represent the only archaea known to oxidize elemental sulfur, and their evolutionary history provides a framework to understand the development of chemolithotrophic growth by sulfur oxidation. Here, we evaluate the sulfur oxidation phenotype of Sulfolobaceae species and leverage comparative genomic and transcriptomic analysis to identify the key genes linked to sulfur oxidation. Metabolic engineering of the obligate heterotroph Sulfolobus acidocaldarius revealed that the known cytoplasmic components of sulfur oxidation alone are not sufficient to drive prolific sulfur oxidation. Imaging analysis showed that Sulfolobaceae species maintain proximity to the sulfur surface but do not necessarily contact the substrate directly. This indicates that a soluble form of sulfur must be transported to initiate cytoplasmic sulfur oxidation. Conservation patterns and transcriptomic response implicate an extracellular tetrathionate hydrolase and putative thiosulfate transporter in a newly proposed mechanism of sulfur acquisition in the Sulfolobaceae.IMPORTANCESulfur is one of the most abundant elements on earth (2.9% by mass), so it makes sense that the earliest biology found a way to use sulfur to create and sustain life. However, beyond evolutionary significance, sulfur and the molecules it comprises have important technological significance, not only in chemicals such as sulfuric acid and in pyritic ores containing critical metals but also as a waste product from oil and gas production. The thermoacidophilic Sulfolobaceae are unique among the archaea as sulfur oxidizers. The trajectory for how sulfur biooxidation arose and evolved can be traced using experimental and bioinformatic analyses of the available genomic data set. Such analysis can also inform the process by which extracellular sulfur is acquired and transported by thermoacidophilic archaea, a phenomenon that is critical to these microorganisms but has yet to be elucidated.
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Affiliation(s)
- Daniel J. Willard
- Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, North Carolina, USA
| | - Mohamad J. H. Manesh
- Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, North Carolina, USA
| | - Ryan G. Bing
- Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, North Carolina, USA
| | - Benjamin H. Alexander
- Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, North Carolina, USA
| | - Robert M. Kelly
- Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, North Carolina, USA
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4
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Falagán C, Sbaffi T, Williams GB, Bargiela R, Dew DW, Hudson-Edwards KA. Nutrient optimization in bioleaching: are we overdosing? Front Microbiol 2024; 15:1359991. [PMID: 38827155 PMCID: PMC11140130 DOI: 10.3389/fmicb.2024.1359991] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2023] [Accepted: 03/13/2024] [Indexed: 06/04/2024] Open
Abstract
The general trend in biomining (i.e., bioleaching and biooxidation) is the use of media with high concentrations of the nutrients (nitrogen as ammonium, phosphorous as phosphate, and K), which are considered to be essential for microbial growth. The depletion of any of the nutrients would affect negatively the bioleaching (and biooxidation) capacity of the microorganisms, so the formulation of the different media ensures that there is a surplus of nutrients. However, some of these nutrients (e.g., phosphate, K) may be already present in the ore and are made available to the microorganisms when the ore is exposed to the low-pH media used during bioleaching. The effect of phosphate addition (109 mg/L) and depletion on the bioleaching of low-grade sulfidic ore alongside the determination of ammonium (i.e., 25 mg/L, 50 mg/L, 109 mg/L, 409 mg/L, and 874 g/L) requirements were studied. The results of the experiments presented showed that the addition of phosphate did not have any effect on the bioleaching of the low-grade sulfidic ore while the addition of ammonium was necessary to obtain higher redox potentials (>650 mV vs. Ag/AgCl) and higher metal (Co, Cu, Ni, and Zn) dissolutions. Temperature was the factor that shaped the microbial communities, at 30°C, the microbial community at the end of all the experiments was dominated by Acidithiobacillus sp. as well as at 42°C, except when nutrients were not added and Sulfobacillus sp. was the dominant microorganism. At 55°C, DNA recovery was unsuccessful, and at 60°C, the microbial communities were dominated by Sulfolobus sp. In conclusion, the amount of nutrients in bioleaching could be reduced significantly to achieve the redox potentials and metal dissolution desired in bioleaching without affecting the microbial communities and bioleaching efficiencies.
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Affiliation(s)
- Carmen Falagán
- Environment & Sustainability Institute and Camborne School of Mines, University of Exeter, Cornwall, United Kingdom
| | - Tomasa Sbaffi
- Molecular Ecology Group, Water Research Institute (IRSA), National Research Council of Italy (CNR), Rome, Italy
- National Biodiversity Future Centre, NBFC, Palermo, Italy
| | - Gwion B. Williams
- Centre for Environmental Biotechnology (CEB), School of Natural Sciences, Bangor University, Bangor, United Kingdom
| | - Rafael Bargiela
- Centre for Environmental Biotechnology (CEB), School of Natural Sciences, Bangor University, Bangor, United Kingdom
| | - David W. Dew
- Environment & Sustainability Institute and Camborne School of Mines, University of Exeter, Cornwall, United Kingdom
| | - Karen A. Hudson-Edwards
- Environment & Sustainability Institute and Camborne School of Mines, University of Exeter, Cornwall, United Kingdom
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5
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Willard DJ, Manesh MJH, Bing RG, Kelly RM. Complete genome sequence for the thermoacidophilic archaeon Sulfuracidifex (f . Sulfolobus) metallicus DSM 6482. Microbiol Resour Announc 2024; 13:e0098123. [PMID: 38054707 PMCID: PMC10793343 DOI: 10.1128/mra.00981-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2023] [Accepted: 11/08/2023] [Indexed: 12/07/2023] Open
Abstract
Reported here is the complete genome sequence (2,191,724 bp) for the thermoacidophilic archaeon Sulfuracidifex (f. Sulfolobus) metallicus DSM 6482 (Topt 65°C, pHopt 2.0). This obligately chemolithoautotrophic microorganism is a prolific metal and sulfur oxidizer and has application in metal bioleaching operations. A multi-assembly reconciliation approach enabled closure of the genome.
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Affiliation(s)
- Daniel J. Willard
- Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, North Carolina, USA
| | - Mohamad J. H. Manesh
- Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, North Carolina, USA
| | - Ryan G. Bing
- Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, North Carolina, USA
| | - Robert M. Kelly
- Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, North Carolina, USA
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6
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Manesh MJH, Willard DJ, Lewis AM, Kelly RM. Extremely thermoacidophilic archaea for metal bioleaching: What do their genomes tell Us? BIORESOURCE TECHNOLOGY 2024; 391:129988. [PMID: 37949149 DOI: 10.1016/j.biortech.2023.129988] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/11/2023] [Revised: 11/03/2023] [Accepted: 11/03/2023] [Indexed: 11/12/2023]
Abstract
Elevated temperatures favor bioleaching processes through faster kinetics, more favorable mineral chemistry, lower cooling requirements, and less surface passivation. Extremely thermoacidophilic archaea from the order Sulfolobales exhibit novel mechanisms for bioleaching metals from ores and have great potential. Genome sequences of many extreme thermoacidophiles are now available and provide new insights into their biochemistry, metabolism, physiology and ecology as these relate to metal mobilization from ores. Although there are some molecular genetic tools available for extreme thermoacidophiles, further development of these is sorely needed to advance the study and application of these archaea for bioleaching applications. The evolving landscape for bioleaching technologies at high temperatures merits a closer look through a genomic lens at what is currently possible and what lies ahead in terms of new developments and emerging opportunities. The need for critical metals and the diminishing primary deposits for copper should provide incentives for high temperature bioleaching.
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Affiliation(s)
- Mohamad J H Manesh
- Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, NC 27695-7905, USA
| | - Daniel J Willard
- Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, NC 27695-7905, USA
| | - April M Lewis
- Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, NC 27695-7905, USA
| | - Robert M Kelly
- Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, NC 27695-7905, USA.
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7
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Sand W, Schippers A, Hedrich S, Vera M. Progress in bioleaching: fundamentals and mechanisms of microbial metal sulfide oxidation - part A. Appl Microbiol Biotechnol 2022; 106:6933-6952. [PMID: 36194263 PMCID: PMC9592645 DOI: 10.1007/s00253-022-12168-7] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2022] [Revised: 08/31/2022] [Accepted: 09/01/2022] [Indexed: 11/30/2022]
Abstract
Abstract Bioleaching of metal sulfides is performed by diverse microorganisms. The dissolution of metal sulfides occurs via two chemical pathways, either the thiosulfate or the polysulfide pathway. These are determined by the metal sulfides’ mineralogy and their acid solubility. The microbial cell enables metal sulfide dissolution via oxidation of iron(II) ions and inorganic sulfur compounds. Thereby, the metal sulfide attacking agents iron(III) ions and protons are generated. Cells are active either in a planktonic state or attached to the mineral surface, forming biofilms. This review, as an update of the previous one (Vera et al., 2013a), summarizes some recent discoveries relevant to bioleaching microorganisms, contributing to a better understanding of their lifestyle. These comprise phylogeny, chemical pathways, surface science, biochemistry of iron and sulfur metabolism, anaerobic metabolism, cell–cell communication, molecular biology, and biofilm lifestyle. Recent advances from genetic engineering applied to bioleaching microorganisms will allow in the future to better understand important aspects of their physiology, as well as to open new possibilities for synthetic biology applications of leaching microbial consortia. Key points • Leaching of metal sulfides is strongly enhanced by microorganisms • Biofilm formation and extracellular polymer production influences bioleaching • Cell interactions in mixed bioleaching cultures are key for process optimization
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Affiliation(s)
- Wolfgang Sand
- Institute of Biosciences, TU Bergakademie Freiberg, Freiberg, Germany. .,Faculty of Chemistry, University Duisburg-Essen, Essen, Germany.
| | - Axel Schippers
- Bundesanstalt für Geowissenschaften und Rohstoffe (BGR), Hannover, Germany
| | - Sabrina Hedrich
- Institute of Biosciences, TU Bergakademie Freiberg, Freiberg, Germany
| | - Mario Vera
- Instituto de Ingeniería Biológica y Médica, Escuelas de Ingeniería, Medicina y Ciencias Biológicas, Pontificia Universidad Católica de Chile, Santiago, Chile. .,Departamento de Ingeniería Hidráulica y Ambiental, Escuela de Ingeniería, Pontificia Universidad Católica de Chile, Santiago, Chile.
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8
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Kato S, Ogasawara A, Itoh T, Sakai HD, Shimizu M, Yuki M, Kaneko M, Takashina T, Ohkuma M. Nanobdella aerobiophila gen. nov., sp. nov., a thermoacidophilic, obligate ectosymbiotic archaeon, and proposal of Nanobdellaceae fam. nov., Nanobdellales ord. nov. and Nanobdellia class. nov. Int J Syst Evol Microbiol 2022; 72. [DOI: 10.1099/ijsem.0.005489] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A co-culture of a novel thermoacidophilic, obligate symbiotic archaeon, designated as strain MJ1T, with its specific host archaeon
Metallosphaera sedula
strain MJ1HA was obtained from a terrestrial hot spring in Japan. Strain MJ1T grew in the co-culture under aerobic conditions. Coccoid cells of strain MJ1T were 200–500 nm in diameter, and attached to the MJ1HA cells in the co-culture. The ranges and optima of the growth temperature and pH of strain MJ1T in the co-culture were 60–75 °C (optimum, 65–70 °C) and pH 1.0–4.0 (optimum, pH 2.5), respectively. Core lipids of dialkyl glycerol tetraethers (GDGT)−3 and GDGT-4 were highly abundant in MJ1T cells concentrated from the co-culture. Strain MJ1T has a small genome (0.67 Mbp) lacking genes for biosynthesis of essential biomolecules, such as nucleotides, lipids and ATP. The genomic DNA G+C content was 24.9 mol%. The 16S rRNA gene sequence of strain MJ1T was most closely related to that of the cultivated species, ‘Nanopusillus acidilobi’ strain N7A (85.8 % similarity). Based on phylogenetic and physiological characteristics, we propose the name Nanobdella aerobiophila gen. nov., sp. nov. to accommodate the strain MJ1T (=JCM 33616T=DSM 111728T). In addition, we propose the names Nanobdellaceae fam. nov., Nanobdellales ord. nov., and Nanobdellia class. nov. to accommodate the novel genus.
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Affiliation(s)
- Shingo Kato
- Japan Collection of Microorganisms, RIKEN BioResource Research Center, Tsukuba, Ibaraki 305-0074, Japan
| | - Ayaka Ogasawara
- Graduate School of Life Sciences, Toyo University, Oura, Gunma 374-0193, Japan
- Japan Collection of Microorganisms, RIKEN BioResource Research Center, Tsukuba, Ibaraki 305-0074, Japan
| | - Takashi Itoh
- Japan Collection of Microorganisms, RIKEN BioResource Research Center, Tsukuba, Ibaraki 305-0074, Japan
| | - Hiroyuki D. Sakai
- Present address: Faculty of Science and Engineering, Soka University, Tokyo 192-8577, Hachioji, Japan
- Japan Collection of Microorganisms, RIKEN BioResource Research Center, Tsukuba, Ibaraki 305-0074, Japan
| | - Michiru Shimizu
- Japan Collection of Microorganisms, RIKEN BioResource Research Center, Tsukuba, Ibaraki 305-0074, Japan
| | - Masahiro Yuki
- Japan Collection of Microorganisms, RIKEN BioResource Research Center, Tsukuba, Ibaraki 305-0074, Japan
| | - Masanori Kaneko
- Research Institute for Geo-Resources and Environment, National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba, 305-8567, Japan
| | - Tomonori Takashina
- Graduate School of Life Sciences, Toyo University, Oura, Gunma 374-0193, Japan
| | - Moriya Ohkuma
- Japan Collection of Microorganisms, RIKEN BioResource Research Center, Tsukuba, Ibaraki 305-0074, Japan
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9
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Sakai HD, Nakamura K, Kurosawa N. Stygiolobus caldivivus sp. nov., a facultatively anaerobic hyperthermophilic archaeon isolated from the Unzen hot spring in Japan. Int J Syst Evol Microbiol 2022; 72. [DOI: 10.1099/ijsem.0.005486] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A novel hyperthermophilic, acidophilic and facultatively anaerobic archaeon, strain KN-1T, was isolated from Unzen hot spring in Japan and characterized. The cells of KN-1T were irregular cocci with a diameter of 1.0–3.0 µm that grew at 55–87.5 °C (optimum: 75 °C) and pH 1.0–5.5 (optimum: 3.0). Chemolithoautotrophic growth of KN-1T occurred in the presence of S0 or H2 under oxic conditions. Under anoxic conditions, KN-1T grew with S0, ferric citrate and FeCl3 as electron acceptors. A phylogenetic analysis of 16S rRNA gene sequences showed that the species most closely related to KN-1T was
Stygiolobus azoricus
JCM 9 021T, with 98.9 % sequence identity, indicating that strain KN-1T belongs to the genus
Stygiolobus
. This genus has been considered to consist of obligate anaerobes since its description in 1991. However, KN-1T grew under oxic, microoxic and anoxic conditions. Moreover, KN-1Tutilized various complex substrates and some sugars as carbon or energy sources, which is also different from
S. azoricus
JCM 9 021T. The average nucleotide identity and amino acid identity values between KN-1T and
S. azoricus
JCM 9 021T were 79.4 and 76.1 %, respectively, indicating that KN-1T represents a novel species. Its main polar lipids were calditoglycerocaldarchaeol and caldarchaeol, and its DNA G+C content was 40.1 mol%. We also found that
S. azoricus
JCM 9021T grew under microoxic conditions in the presence of H2 as an electron donor, indicating that this genus does not comprise obligate anaerobes. Based on this polyphasic taxonomic analysis, we propose the novel species, Stygiolobus caldivivus sp. nov., whose type strain is KN-1T (=JCM 34 622T=KCTC 4 293T).
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Affiliation(s)
- Hiroyuki D. Sakai
- Department of Science and Engineering for Sustainable Innovation, Faculty of Science and Engineering, Soka University, Hachioji, Tokyo, Japan
| | - Koichi Nakamura
- Department of Environmental Engineering for Symbiosis, Graduate School of Science and Engineering, Soka University, Hachioji, Tokyo, Japan
| | - Norio Kurosawa
- Department of Environmental Engineering for Symbiosis, Graduate School of Science and Engineering, Soka University, Hachioji, Tokyo, Japan
- Department of Science and Engineering for Sustainable Innovation, Faculty of Science and Engineering, Soka University, Hachioji, Tokyo, Japan
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10
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Chromosome organization affects genome evolution in Sulfolobus archaea. Nat Microbiol 2022; 7:820-830. [PMID: 35618771 DOI: 10.1038/s41564-022-01127-7] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2021] [Accepted: 04/21/2022] [Indexed: 12/16/2022]
Abstract
In all organisms, the DNA sequence and the structural organization of chromosomes affect gene expression. The extremely thermophilic crenarchaeon Sulfolobus has one circular chromosome with three origins of replication. We previously revealed that this chromosome has defined A and B compartments that have high and low gene expression, respectively. As well as higher levels of gene expression, the A compartment contains the origins of replication. To evaluate the impact of three-dimensional organization on genome evolution, we characterized the effect of replication origins and compartmentalization on primary sequence evolution in eleven Sulfolobus species. Using single-nucleotide polymorphism analyses, we found that distance from an origin of replication was associated with increased mutation rates in the B but not in the A compartment. The enhanced polymorphisms distal to replication origins suggest that replication termination may have a causal role in their generation. Further mutational analyses revealed that the sequences in the A compartment are less likely to be mutated, and that there is stronger purifying selection than in the B compartment. Finally, we applied the Assay for Transposase-Accessible Chromatin using sequencing (ATAC-seq) to show that the B compartment is less accessible than the A compartment. Taken together, our data suggest that compartmentalization of chromosomal DNA can influence chromosome evolution in Sulfolobus. We propose that the A compartment serves as a haven for stable maintenance of gene sequences, while sequences in the B compartment can be diversified.
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11
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Liu LJ, Jiang Z, Wang P, Qin YL, Xu W, Wang Y, Liu SJ, Jiang CY. Physiology, Taxonomy, and Sulfur Metabolism of the Sulfolobales, an Order of Thermoacidophilic Archaea. Front Microbiol 2021; 12:768283. [PMID: 34721370 PMCID: PMC8551704 DOI: 10.3389/fmicb.2021.768283] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2021] [Accepted: 09/22/2021] [Indexed: 11/13/2022] Open
Abstract
The order Sulfolobales (phylum Crenarchaeota) is a group of thermoacidophilic archaea. The first member of the Sulfolobales was discovered in 1972, and current 23 species are validly named under the International Code of Nomenclature of Prokaryotes. The majority of members of the Sulfolobales is obligately or facultatively chemolithoautotrophic. When they grow autotrophically, elemental sulfur or reduced inorganic sulfur compounds are their energy sources. Therefore, sulfur metabolism is the most important physiological characteristic of the Sulfolobales. The functions of some enzymes and proteins involved in sulfur reduction, sulfur oxidation, sulfide oxidation, thiosulfate oxidation, sulfite oxidation, tetrathionate hydrolysis, and sulfur trafficking have been determined. In this review, we describe current knowledge about the physiology, taxonomy, and sulfur metabolism of the Sulfolobales, and note future challenges in this field.
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Affiliation(s)
- Li-Jun Liu
- School of Basic Medical Science, the Xi'an Key Laboratory of Pathogenic Microorganism and Tumor Immunity, Xi'an Medical University, Xi'an, China.,Key Laboratory of Resources Biology and Biotechnology in Western China, Ministry of Education, College of Life Sciences, Northwest University, Xi'an, China
| | - Zhen Jiang
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Pei Wang
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Ya-Ling Qin
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Wen Xu
- School of Basic Medical Science, the Xi'an Key Laboratory of Pathogenic Microorganism and Tumor Immunity, Xi'an Medical University, Xi'an, China.,Key Laboratory of Resources Biology and Biotechnology in Western China, Ministry of Education, College of Life Sciences, Northwest University, Xi'an, China
| | - Yang Wang
- School of Basic Medical Science, the Xi'an Key Laboratory of Pathogenic Microorganism and Tumor Immunity, Xi'an Medical University, Xi'an, China.,Key Laboratory of Resources Biology and Biotechnology in Western China, Ministry of Education, College of Life Sciences, Northwest University, Xi'an, China
| | - Shuang-Jiang Liu
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Cheng-Ying Jiang
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China.,University of Chinese Academy of Sciences, Beijing, China
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12
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Complete Genome Sequence of a Novel Sulfolobales Archaeon Strain, HS-7, Isolated from the Unzen Hot Spring in Japan. Microbiol Resour Announc 2021; 10:e0058221. [PMID: 34553995 PMCID: PMC8459659 DOI: 10.1128/mra.00582-21] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The order Sulfolobales includes thermoacidophilic archaea that thrive in acidic geothermal environments. A novel Sulfolobales archaeon strain, HS-7, which may represent a novel genus, was isolated from an acidic hot spring in Japan. We report the 2.15-Mb complete genome sequence of strain HS-7.
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Lewis AM, Recalde A, Bräsen C, Counts JA, Nussbaum P, Bost J, Schocke L, Shen L, Willard DJ, Quax TEF, Peeters E, Siebers B, Albers SV, Kelly RM. The biology of thermoacidophilic archaea from the order Sulfolobales. FEMS Microbiol Rev 2021; 45:fuaa063. [PMID: 33476388 PMCID: PMC8557808 DOI: 10.1093/femsre/fuaa063] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2020] [Accepted: 11/26/2020] [Indexed: 12/13/2022] Open
Abstract
Thermoacidophilic archaea belonging to the order Sulfolobales thrive in extreme biotopes, such as sulfuric hot springs and ore deposits. These microorganisms have been model systems for understanding life in extreme environments, as well as for probing the evolution of both molecular genetic processes and central metabolic pathways. Thermoacidophiles, such as the Sulfolobales, use typical microbial responses to persist in hot acid (e.g. motility, stress response, biofilm formation), albeit with some unusual twists. They also exhibit unique physiological features, including iron and sulfur chemolithoautotrophy, that differentiate them from much of the microbial world. Although first discovered >50 years ago, it was not until recently that genome sequence data and facile genetic tools have been developed for species in the Sulfolobales. These advances have not only opened up ways to further probe novel features of these microbes but also paved the way for their potential biotechnological applications. Discussed here are the nuances of the thermoacidophilic lifestyle of the Sulfolobales, including their evolutionary placement, cell biology, survival strategies, genetic tools, metabolic processes and physiological attributes together with how these characteristics make thermoacidophiles ideal platforms for specialized industrial processes.
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Affiliation(s)
- April M Lewis
- Department of Chemical and Biomolecular Engineering, North Carolina State University. Raleigh, NC 27695, USA
| | - Alejandra Recalde
- Institute for Biology, Molecular Biology of Archaea, University of Freiburg, 79104 Freiburg, Germany
| | - Christopher Bräsen
- Department of Molecular Enzyme Technology and Biochemistry, Environmental Microbiology and Biotechnology, and Centre for Water and Environmental Research, University of Duisburg-Essen, 45117 Essen, Germany
| | - James A Counts
- Department of Chemical and Biomolecular Engineering, North Carolina State University. Raleigh, NC 27695, USA
| | - Phillip Nussbaum
- Institute for Biology, Molecular Biology of Archaea, University of Freiburg, 79104 Freiburg, Germany
| | - Jan Bost
- Institute for Biology, Molecular Biology of Archaea, University of Freiburg, 79104 Freiburg, Germany
| | - Larissa Schocke
- Department of Molecular Enzyme Technology and Biochemistry, Environmental Microbiology and Biotechnology, and Centre for Water and Environmental Research, University of Duisburg-Essen, 45117 Essen, Germany
| | - Lu Shen
- Department of Molecular Enzyme Technology and Biochemistry, Environmental Microbiology and Biotechnology, and Centre for Water and Environmental Research, University of Duisburg-Essen, 45117 Essen, Germany
| | - Daniel J Willard
- Department of Chemical and Biomolecular Engineering, North Carolina State University. Raleigh, NC 27695, USA
| | - Tessa E F Quax
- Archaeal Virus–Host Interactions, Faculty of Biology, University of Freiburg, 79104 Freiburg, Germany
| | - Eveline Peeters
- Research Group of Microbiology, Department of Bioengineering Sciences, Vrije Universiteit Brussel, 1050 Brussels, Belgium
| | - Bettina Siebers
- Department of Molecular Enzyme Technology and Biochemistry, Environmental Microbiology and Biotechnology, and Centre for Water and Environmental Research, University of Duisburg-Essen, 45117 Essen, Germany
| | - Sonja-Verena Albers
- Institute for Biology, Molecular Biology of Archaea, University of Freiburg, 79104 Freiburg, Germany
| | - Robert M Kelly
- Department of Chemical and Biomolecular Engineering, North Carolina State University. Raleigh, NC 27695, USA
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Counts JA, Willard DJ, Kelly RM. Life in hot acid: a genome-based reassessment of the archaeal order Sulfolobales. Environ Microbiol 2021; 23:3568-3584. [PMID: 32776389 PMCID: PMC10560490 DOI: 10.1111/1462-2920.15189] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2020] [Revised: 07/31/2020] [Accepted: 08/06/2020] [Indexed: 01/07/2023]
Abstract
The order Sulfolobales was one of the first named Archaeal lineages, with globally distributed members from terrestrial thermal acid springs (pH < 4; T > 65°C). The Sulfolobales represent broad metabolic capabilities, ranging from lithotrophy, based on inorganic iron and sulfur biotransformations, to autotrophy, to chemoheterotrophy in less acidophilic species. Components of the 3-hydroxypropionate/4-hydroxybutyrate carbon fixation cycle, as well as sulfur oxidation, are nearly universally conserved, although dissimilatory sulfur reduction and disproportionation (Acidianus, Stygiolobus and Sulfurisphaera) and iron oxidation (Acidianus, Metallosphaera, Sulfurisphaera, Sulfuracidifex and Sulfodiicoccus) are limited to fewer lineages. Lithotrophic marker genes appear more often in highly acidophilic lineages. Despite the presence of facultative anaerobes and one confirmed obligate anaerobe, oxidase complexes (fox, sox, dox and a new putative cytochrome bd) are prevalent in many species (even facultative/obligate anaerobes), suggesting a key role for oxygen among the Sulfolobales. The presence of fox genes tracks with a putative antioxidant OsmC family peroxiredoxin, an indicator of oxidative stress derived from mixing reactive metals and oxygen. Extreme acidophily appears to track inversely with heterotrophy but directly with lithotrophy. Recent phylogenetic re-organization efforts are supported by the comparative genomics here, although several changes are proposed, including the expansion of the genus Saccharolobus.
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Affiliation(s)
- James A. Counts
- Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, NC 27695 USA
| | - Daniel J. Willard
- Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, NC 27695 USA
| | - Robert M. Kelly
- Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, NC 27695 USA
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