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Chiu BK, Waldbauer J, Elling FJ, Mete ÖZ, Zhang L, Pearson A, Eggleston EM, Leavitt WD. Membrane lipid and expression responses of Saccharolobus islandicus REY15A to acid and cold stress. Front Microbiol 2023; 14:1219779. [PMID: 37649629 PMCID: PMC10465181 DOI: 10.3389/fmicb.2023.1219779] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2023] [Accepted: 07/24/2023] [Indexed: 09/01/2023] Open
Abstract
Archaea adjust the number of cyclopentane rings in their glycerol dibiphytanyl glycerol tetraether (GDGT) membrane lipids as a homeostatic response to environmental stressors such as temperature, pH, and energy availability shifts. However, archaeal expression patterns that correspond with changes in GDGT composition are less understood. Here we characterize the acid and cold stress responses of the thermoacidophilic crenarchaeon Saccharolobus islandicus REY15A using growth rates, core GDGT lipid profiles, transcriptomics and proteomics. We show that both stressors result in impaired growth, lower average GDGT cyclization, and differences in gene and protein expression. Transcription data revealed differential expression of the GDGT ring synthase grsB in response to both acid stress and cold stress. Although the GDGT ring synthase encoded by grsB forms highly cyclized GDGTs with ≥5 ring moieties, S. islandicus grsB upregulation under acidic pH conditions did not correspond with increased abundances of highly cyclized GDGTs. Our observations highlight the inability to predict GDGT changes from transcription data alone. Broader analysis of transcriptomic data revealed that S. islandicus differentially expresses many of the same transcripts in response to both acid and cold stress. These included upregulation of several biosynthetic pathways and downregulation of oxidative phosphorylation and motility. Transcript responses specific to either of the two stressors tested here included upregulation of genes related to proton pumping and molecular turnover in acid stress conditions and upregulation of transposases in cold stress conditions. Overall, our study provides a comprehensive understanding of the GDGT modifications and differential expression characteristic of the acid stress and cold stress responses in S. islandicus.
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Affiliation(s)
- Beverly K. Chiu
- Department of Earth Sciences, Dartmouth College, Hanover, NH, United States
| | - Jacob Waldbauer
- Department of the Geophysical Sciences, The University of Chicago, Chicago, IL, United States
| | - Felix J. Elling
- Department of Earth and Planetary Sciences, Harvard University, Cambridge, MA, United States
- Leibniz-Laboratory for Radiometric Dating and Isotope Research, Kiel University, Kiel, Germany
| | - Öykü Z. Mete
- Department of Earth Sciences, Dartmouth College, Hanover, NH, United States
- Department of Earth and Planetary Sciences, Harvard University, Cambridge, MA, United States
| | - Lichun Zhang
- Department of the Geophysical Sciences, The University of Chicago, Chicago, IL, United States
| | - Ann Pearson
- Department of Earth and Planetary Sciences, Harvard University, Cambridge, MA, United States
| | - Erin M. Eggleston
- Department of Biology, Middlebury College, Middlebury, VT, United States
| | - William D. Leavitt
- Department of Earth Sciences, Dartmouth College, Hanover, NH, United States
- Department of Chemistry, Dartmouth College, Hanover, NH, United States
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2
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Sazykin IS, Sazykina MA. The role of oxidative stress in genome destabilization and adaptive evolution of bacteria. Gene X 2023; 857:147170. [PMID: 36623672 DOI: 10.1016/j.gene.2023.147170] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2022] [Revised: 12/14/2022] [Accepted: 01/03/2023] [Indexed: 01/09/2023] Open
Abstract
The review is devoted to bacterial genome destabilization by oxidative stress. The article discusses the main groups of substances causing such stress. Stress regulons involved in destabilization of genetic material and mechanisms enhancing mutagenesis, bacterial genome rearrangements, and horizontal gene transfer, induced by oxidative damage to cell components are also considered. Based on the analysis of publications, it can be claimed that rapid development of new food substrates and ecological niches by microorganisms occurs due to acceleration of genetic changes induced by oxidative stress, mediated by several stress regulons (SOS, RpoS and RpoE) and under selective pressure. The authors conclude that non-lethal oxidative stress is probably-one of the fundamental processes that guide evolution of prokaryotes and a powerful universal trigger for adaptive destabilization of bacterial genome under changing environmental conditions.
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Affiliation(s)
- I S Sazykin
- Southern Federal University, 194/2 Stachki Avenue, Rostov-on-Don 344090, Russian Federation
| | - M A Sazykina
- Southern Federal University, 194/2 Stachki Avenue, Rostov-on-Don 344090, Russian Federation.
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3
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Liu R, Zhou H. Growth in ever-increasing acidity condition enhanced the adaptation and bioleaching ability of Leptospirillum ferriphilum. Int Microbiol 2022; 25:541-550. [PMID: 35175436 DOI: 10.1007/s10123-021-00227-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2021] [Revised: 11/18/2021] [Accepted: 12/02/2021] [Indexed: 11/26/2022]
Abstract
Low pH eliminated the jarosite accumulation and improved the interfacial reaction rate during the bioleaching process. However, high acidity tends to make environments less hospitable, even for organisms that live in extreme places, so a great challenge existed for bioleaching at low pH conditions. This study demonstrated that the adaption and bioleaching ability of Leptospirillum ferriphilum could be improved after the long-term adaptive evolution of the community under acidity conditions. It was found that the acidity-adapted strain showed robust ferrous iron oxidation activity in wider pH, high concentration of ferrous iron, and lower temperature. Although the enhancement for heavy metal tolerance was limited, the resistance for MgSO4, Na2SO4, and organic matter was stimulative. More importantly, both pyrite and printed circuit board bioleaching revealed the higher bioleaching ability of the acid-resistant strain. These adaptation and bioleaching details provided an available approach for the improvement of bioleaching techniques.
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Affiliation(s)
- Ronghui Liu
- School of Minerals Processing and Bioengineering, Central South University, Changsha, China
- School of Microelectronic, Southern University of Science and Technology, Shenzhen, China
| | - Hongbo Zhou
- School of Minerals Processing and Bioengineering, Central South University, Changsha, China.
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4
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Physiological Characterization of Sulfolobus acidocaldarius in a Controlled Bioreactor Environment. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2021; 18:ijerph18115532. [PMID: 34064179 PMCID: PMC8196767 DOI: 10.3390/ijerph18115532] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/18/2021] [Revised: 05/18/2021] [Accepted: 05/19/2021] [Indexed: 01/28/2023]
Abstract
The crenarchaeal model organism Sulfolobus acidocaldarius is typically cultivated in shake flasks. Although shake flasks represent the state-of-the-art for the cultivation of this microorganism, in these systems crucial process parameters, like pH or substrate availability, are only set initially, but cannot be controlled during the cultivation process. As a result, a thorough characterization of growth parameters under controlled conditions is still missing for S. acidocaldarius. In this study, we conducted chemostat cultivations at 75 °C using a growth medium containing L-glutamate and D-glucose as main carbon sources. Different pH values and dilution rates were applied with the goal to physiologically characterize the organism in a controlled bioreactor environment. Under these controlled conditions a pH optimum of 3.0 was determined. Washout of the cells occurred at a dilution rate of 0.097 h−1 and the optimal productivity of biomass was observed at a dilution rate of 0.062 h−1. While both carbon sources were taken up by S. acidocaldarius concomitantly, a 6.6-fold higher affinity for L-glutamate was shown. When exposed to suboptimal growth conditions, S. acidocaldarius reacted with a change in the respiratory behavior and an increased trehalose production rate in addition to a decreased growth rate.
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5
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Hart C, Gorman-Lewis D. Energetics of Acidianus ambivalens growth in response to oxygen availability. GEOBIOLOGY 2021; 19:48-62. [PMID: 32902110 DOI: 10.1111/gbi.12413] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/30/2019] [Revised: 07/30/2020] [Accepted: 08/02/2020] [Indexed: 06/11/2023]
Abstract
All life requires energy to drive metabolic reactions such as growth and cell maintenance; therefore, fluctuations in energy availability can alter microbial activity. There is a gap in our knowledge concerning how energy availability affects the growth of extreme chemolithoautotrophs. Toward this end, we investigated the growth of thermoacidophile Acidianus ambivalens during sulfur oxidation under aerobic to microaerophilic conditions. Calorimetry was used to measure enthalpy (ΔHinc ) of microbial activity, and chemical changes in growth media were measured to calculate Gibbs energy change (ΔGinc ) during incubation. In all experiments, Gibbs energy was primarily dissipated through the release of heat, which suggests enthalpy-driven growth. In microaerophilic conditions, growth was significantly more efficient in terms of biomass yield (defined as C-mol biomass per mole sulfur consumed) and resulted in lower ΔGinc and ΔHinc . ΔGinc in oxygen-limited (OL) and oxygen- and CO2 -limited (OCL) microaerophilic growth conditions resulted in averages of -1.44 × 103 kJ/C-mol and -7.56 × 102 kJ/C-mol, respectively, and average ΔHinc values of -1.11 × 105 kJ/C-mol and -4.43 × 104 kJ/C-mol, respectively. High-oxygen experiments resulted in lower biomass yield values, an increase in ΔGinc to -1.71 × 104 kJ/C-mol, and more exothermic ΔHinc values of -4.71 × 105 kJ/C-mol. The observed inefficiency in high-oxygen conditions may suggest larger maintenance energy demands due to oxidative stresses and a preference for growth in microaerophilic environments.
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Affiliation(s)
- Chloe Hart
- Department of Earth and Space Sciences, University of Washington, Seattle, WA, USA
| | - Drew Gorman-Lewis
- Department of Earth and Space Sciences, University of Washington, Seattle, WA, USA
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6
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Sun L, Gong M, Lv X, Huang Z, Gu Y, Li J, Du G, Liu L. Current advance in biological production of short-chain organic acid. Appl Microbiol Biotechnol 2020; 104:9109-9124. [DOI: 10.1007/s00253-020-10917-0] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2020] [Revised: 09/14/2020] [Accepted: 09/17/2020] [Indexed: 12/31/2022]
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The Cell Membrane of Sulfolobus spp.-Homeoviscous Adaption and Biotechnological Applications. Int J Mol Sci 2020; 21:ijms21113935. [PMID: 32486295 PMCID: PMC7312580 DOI: 10.3390/ijms21113935] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2020] [Revised: 05/27/2020] [Accepted: 05/29/2020] [Indexed: 12/20/2022] Open
Abstract
The microbial cell membrane is affected by physicochemical parameters, such as temperature and pH, but also by the specific growth rate of the host organism. Homeoviscous adaption describes the process of maintaining membrane fluidity and permeability throughout these environmental changes. Archaea, and thereby, Sulfolobus spp. exhibit a unique lipid composition of ether lipids, which are altered in regard to the ratio of diether to tetraether lipids, number of cyclopentane rings and type of head groups, as a coping mechanism against environmental changes. The main biotechnological application of the membrane lipids of Sulfolobus spp. are so called archaeosomes. Archaeosomes are liposomes which are fully or partly generated from archaeal lipids and harbor the potential to be used as drug delivery systems for vaccines, proteins, peptides and nucleic acids. This review summarizes the influence of environmental parameters on the cell membrane of Sulfolobus spp. and the biotechnological applications of their membrane lipids.
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8
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Kunka KS, Griffith JM, Holdener C, Bischof KM, Li H, DasSarma P, DasSarma S, Slonczewski JL. Acid Experimental Evolution of the Haloarchaeon Halobacterium sp. NRC-1 Selects Mutations Affecting Arginine Transport and Catabolism. Front Microbiol 2020; 11:535. [PMID: 32390952 PMCID: PMC7193027 DOI: 10.3389/fmicb.2020.00535] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2019] [Accepted: 03/12/2020] [Indexed: 11/13/2022] Open
Abstract
Halobacterium sp. NRC-1 (NRC-1) is an extremely halophilic archaeon that is adapted to multiple stressors such as UV, ionizing radiation and arsenic exposure; it is considered a model organism for the feasibility of microbial life in iron-rich brine on Mars. We conducted experimental evolution of NRC-1 under acid and iron stress. NRC-1 was serially cultured in CM+ medium modified by four conditions: optimal pH (pH 7.5), acid stress (pH 6.3), iron amendment (600 μM ferrous sulfate, pH 7.5), and acid plus iron (pH 6.3, with 600 μM ferrous sulfate). For each condition, four independent lineages of evolving populations were propagated. After 500 generations, 16 clones were isolated for phenotypic characterization and genomic sequencing. Genome sequences of all 16 clones revealed 378 mutations, of which 90% were haloarchaeal insertion sequences (ISH) and ISH-mediated large deletions. This proportion of ISH events in NRC-1 was five-fold greater than that reported for comparable evolution of Escherichia coli. One acid-evolved clone had increased fitness compared to the ancestral strain when cultured at low pH. Seven of eight acid-evolved clones had a mutation within or upstream of arcD, which encodes an arginine-ornithine antiporter; no non-acid adapted strains had arcD mutations. Mutations also affected the arcR regulator of arginine catabolism, which protects bacteria from acid stress by release of ammonia. Two acid-adapted strains shared a common mutation in bop, which encodes bacterio-opsin, apoprotein for the bacteriorhodopsin light-driven proton pump. Thus, in the haloarchaeon NRC-1, as in bacteria, pH adaptation was associated with genes involved in arginine catabolism and proton transport. Our study is among the first to report experimental evolution with multiple resequenced genomes of an archaeon. Haloarchaea are polyextremophiles capable of growth under environmental conditions such as concentrated NaCl and desiccation, but little is known about pH stress. Interesting parallels appear between the molecular basis of pH adaptation in NRC-1 and in bacteria, particularly the acid-responsive arginine-ornithine system found in oral streptococci.
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Affiliation(s)
- Karina S. Kunka
- Department of Biology, Kenyon College, Gambier, OH, United States
- Institute of Marine and Environmental Technology, Department of Microbiology and Immunology, University of Maryland School of Medicine, Baltimore, MD, United States
| | - Jessie M. Griffith
- Department of Biology, Kenyon College, Gambier, OH, United States
- Institute of Marine and Environmental Technology, Department of Microbiology and Immunology, University of Maryland School of Medicine, Baltimore, MD, United States
| | - Chase Holdener
- Department of Biology, Kenyon College, Gambier, OH, United States
| | | | - Haofan Li
- Department of Biology, Kenyon College, Gambier, OH, United States
| | - Priya DasSarma
- Institute of Marine and Environmental Technology, Department of Microbiology and Immunology, University of Maryland School of Medicine, Baltimore, MD, United States
| | - Shiladitya DasSarma
- Institute of Marine and Environmental Technology, Department of Microbiology and Immunology, University of Maryland School of Medicine, Baltimore, MD, United States
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9
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Eichler J. Modifying Post‐Translational Modifications: A Strategy Used by Archaea for Adapting to Changing Environments? Bioessays 2020; 42:e1900207. [DOI: 10.1002/bies.201900207] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2019] [Revised: 12/15/2019] [Indexed: 01/07/2023]
Affiliation(s)
- Jerry Eichler
- Department of Life SciencesBen Gurion University of the Negev Beersheva 84105 Israel
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10
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Suzuki S, Kurosawa N. Participation of UV-regulated Genes in the Response to Helix-distorting DNA Damage in the Thermoacidophilic Crenarchaeon Sulfolobus acidocaldarius. Microbes Environ 2019; 34:363-373. [PMID: 31548441 PMCID: PMC6934391 DOI: 10.1264/jsme2.me19055] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
Several species of Sulfolobales have been used as model organisms in the study of response mechanisms to ultraviolet (UV) irradiation in hyperthermophilic crenarchaea. To date, the transcriptional responses of genes involved in the initiation of DNA replication, transcriptional regulation, protein phosphorylation, and hypothetical function have been observed in Sulfolobales species after UV irradiation. However, due to the absence of knockout experiments, the functions of these genes under in situ UV irradiation have not yet been demonstrated. In the present study, we constructed five gene knockout strains (cdc6-2, tfb3, rio1, and two genes encoding the hypothetical proteins, Saci_0951 and Saci_1302) of Sulfolobus acidocaldarius and examined their sensitivities to UV irradiation. The knockout strains exhibited significant sensitivities to UV-B irradiation, indicating that the five UV-regulated genes play an important role in responses to UV irradiation in vivo. Furthermore, Δcdc6-2, Δrio1, ΔSaci_0951, and Δtfb3 were sensitive to a wide variety of helix-distorting DNA lesions, including UV-induced DNA damage, an intra-strand crosslink, and bulky adducts. These results reveal that cdc6-2, tfb3, rio1, and Saci_0951 are play more important roles in broad responses to helix-distorting DNA damage than in specific responses to UV irradiation.
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Affiliation(s)
- Shoji Suzuki
- Department of Science and Engineering for Sustainable Development, Faculty of Science and Engineering, Soka University
| | - Norio Kurosawa
- Department of Science and Engineering for Sustainable Development, Faculty of Science and Engineering, Soka University
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11
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Hackley RK, Schmid AK. Global Transcriptional Programs in Archaea Share Features with the Eukaryotic Environmental Stress Response. J Mol Biol 2019; 431:4147-4166. [PMID: 31437442 PMCID: PMC7419163 DOI: 10.1016/j.jmb.2019.07.029] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2019] [Revised: 07/18/2019] [Accepted: 07/18/2019] [Indexed: 01/06/2023]
Abstract
The environmental stress response (ESR), a global transcriptional program originally identified in yeast, is characterized by a rapid and transient transcriptional response composed of large, oppositely regulated gene clusters. Genes induced during the ESR encode core components of stress tolerance, macromolecular repair, and maintenance of homeostasis. In this review, we investigate the possibility for conservation of the ESR across the eukaryotic and archaeal domains of life. We first re-analyze existing transcriptomics data sets to illustrate that a similar transcriptional response is identifiable in Halobacterium salinarum, an archaeal model organism. To substantiate the archaeal ESR, we calculated gene-by-gene correlations, gene function enrichment, and comparison of temporal dynamics. We note reported examples of variation in the ESR across fungi, then synthesize high-level trends present in expression data of other archaeal species. In particular, we emphasize the need for additional high-throughput time series expression data to further characterize stress-responsive transcriptional programs in the Archaea. Together, this review explores an open question regarding features of global transcriptional stress response programs shared across domains of life.
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Affiliation(s)
- Rylee K Hackley
- Department of Biology, Duke University, Durham, NC 27708, USA; University Program in Genetics and Genomics, Duke University, Durham, NC 27708, USA
| | - Amy K Schmid
- Department of Biology, Duke University, Durham, NC 27708, USA; University Program in Genetics and Genomics, Duke University, Durham, NC 27708, USA; Center for Genomics and Computational Biology, Duke University, Durham, NC 27708, USA.
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12
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Liu R, Chen Y, Tian Z, Mao Z, Cheng H, Zhou H, Wang W. Enhancing microbial community performance on acid resistance by modified adaptive laboratory evolution. BIORESOURCE TECHNOLOGY 2019; 287:121416. [PMID: 31103940 DOI: 10.1016/j.biortech.2019.121416] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/14/2019] [Revised: 04/30/2019] [Accepted: 05/02/2019] [Indexed: 05/09/2023]
Abstract
A new strategy of three-step adaptive laboratory evolution (ALE) was developed to enhance the bioleaching performance of moderately thermophilic consortia. Through consortium construction, directed evolution and chemostat selection, an improved consortium (ALEend) that composed of Leptospirillum ferriphilum (80.32%), Sulfobacillus thermosulfidooxidans (15.82%) and Ferroplasma thermophilum (3.86%) was obtained, showing ferrous iron oxidation rate of 500 mgL-1h-1 and biomass production of 2.0 × 108 cells/mL at pH 0.75. During batch culturing, the ALEend consortium exhibited stable ferrous iron oxidation in wider conditions. PCA indicated that the communities were similar under fluctuating culture conditions, which demonstrated the stable community structure and the reinforced synergistic interactions resulting in the enhanced community performance. Pyrite bioleaching conducted at pH 1.5 and 0.75 revealed that the ALEend consortium extracted 26% and 55% more total iron relative to the original consortium. These findings indicated that the modified ALE may be a promising strategy for microbial community modification to enhance bioleaching.
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Affiliation(s)
- Ronghui Liu
- School of Minerals Processing and Bioengineering, Central South University, Changsha, China
| | - Yanzhi Chen
- South China Institute of Environmental Sciences, Guangzhou, China
| | - Zhuang Tian
- School of Minerals Processing and Bioengineering, Central South University, Changsha, China
| | - Zhenghua Mao
- School of Minerals Processing and Bioengineering, Central South University, Changsha, China
| | - Haina Cheng
- School of Minerals Processing and Bioengineering, Central South University, Changsha, China
| | - Hongbo Zhou
- School of Minerals Processing and Bioengineering, Central South University, Changsha, China.
| | - Wei Wang
- South China Institute of Environmental Sciences, Guangzhou, China
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13
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Blum P, Payne S. Evidence of an Epigenetics System in Archaea. Epigenet Insights 2019; 12:2516865719865280. [PMID: 31384725 PMCID: PMC6664620 DOI: 10.1177/2516865719865280] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2019] [Accepted: 07/01/2019] [Indexed: 12/17/2022] Open
Abstract
Changes in the phenotype of a cell or organism that are heritable but do not
involve changes in DNA sequence are referred to as epigenetic. They occur
primarily through the gain or loss of chemical modification of chromatin protein
or DNA. Epigenetics is therefore a non-Mendelian process. The study of
epigenetics in eukaryotes is expanding with advances in knowledge about the
relationship between mechanism and phenotype and as a requirement for
multicellularity and cancer. However, life also includes other groups or
domains, notably the bacteria and archaea. The occurrence of epigenetics in
these deep lineages is an emerging topic accompanied by controversy. In these
non-eukaryotic organisms, epigenetics is critically important because it
stimulates new evolutionary theory and refines perspective about biological
action.
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Affiliation(s)
- Paul Blum
- School of Biological Science, University of Nebraska-Lincoln, Lincoln, NE, USA.,Department of Microbiology and Toxicology, University of California Santa Cruz, Santa Cruz, CA, USA
| | - Sophie Payne
- School of Biological Science, University of Nebraska-Lincoln, Lincoln, NE, USA.,Department of Microbiology and Toxicology, University of California Santa Cruz, Santa Cruz, CA, USA
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14
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Johnson T, Payne S, Grove R, McCarthy S, Oeltjen E, Mach C, Adamec J, Wilson MA, Van Cott K, Blum P. Methylation deficiency of chromatin proteins is a non-mutational and epigenetic-like trait in evolved lines of the archaeon Sulfolobus solfataricus. J Biol Chem 2019; 294:7821-7832. [PMID: 30918025 PMCID: PMC6514617 DOI: 10.1074/jbc.ra118.006469] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2018] [Revised: 03/01/2019] [Indexed: 11/06/2022] Open
Abstract
Archaea are a distinct and deeply rooted lineage that harbor eukaryotic-like mechanisms, including several that manage chromosome function. In previous work, the thermoacidophilic crenarchaeon, Sulfolobus solfataricus, was subjected to adaptive laboratory evolution to produce three strains, called SARC, with a new heritable trait of super acid resistance. These strains acquired heritable conserved transcriptomes, yet one strain contained no mutations. Homologous recombination without allele replacement at SARC acid resistance genes caused changes in both phenotype and expression of the targeted gene. As recombination displaces chromatin proteins, their involvement was predicted in the SARC trait. Native chromatin proteins are basic and highly abundant and undergo post-translational modification through lysine monomethylation. In this work, their modification states were investigated. In all SARC lines, two chromatin proteins, Cren7 and Sso7d, were consistently undermethylated, whereas other chromatin proteins were unaltered. This pattern was heritable in the absence of selection and independent of transient exposure to acid stress. The bulk of Sso7d was undermethylated at three contiguous N-terminal lysine residues but not at central or C-terminal regions. The N-terminal region formed a solvent-exposed patch located on the opposite side of the binding domain associated with the DNA minor groove. By analogy to eukaryotic histones, this patch could interact with other chromosomal proteins and be modulated by differential post-translational modification. Previous work established an epigenetic-like mechanism of adaptation and inheritance in S. solfataricus The identification of heritable epigenetic marks in this work further supports the occurrence of an epigenetic process in archaea.
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Affiliation(s)
- Tyler Johnson
- From the Beadle Center for Genetics, School of Biological Sciences
| | - Sophie Payne
- From the Beadle Center for Genetics, School of Biological Sciences
| | - Ryan Grove
- the Department of Biochemistry and Redox Biology Center, and
| | - Samuel McCarthy
- From the Beadle Center for Genetics, School of Biological Sciences
| | - Erin Oeltjen
- From the Beadle Center for Genetics, School of Biological Sciences
| | - Collin Mach
- From the Beadle Center for Genetics, School of Biological Sciences
| | - Jiri Adamec
- the Department of Biochemistry and Redox Biology Center, and
| | - Mark A Wilson
- the Department of Biochemistry and Redox Biology Center, and
| | - Kevin Van Cott
- the Department of Chemical and Biomolecular Engineering, University of Nebraska, Lincoln, Nebraska 68588, and
| | - Paul Blum
- From the Beadle Center for Genetics, School of Biological Sciences,
- the Department of Microbiology and Toxicology, University of California, Santa Cruz, California 95064
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15
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Ma L, Wang H, Wu J, Wang Y, Zhang D, Liu X. Metatranscriptomics reveals microbial adaptation and resistance to extreme environment coupling with bioleaching performance. BIORESOURCE TECHNOLOGY 2019; 280:9-17. [PMID: 30743055 DOI: 10.1016/j.biortech.2019.01.117] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/20/2018] [Revised: 01/22/2019] [Accepted: 01/23/2019] [Indexed: 06/09/2023]
Abstract
Chalcopyrite bioleaching by 2, 4 and 6 acidophilic strains with the same inoculation density were studied, respectively. The results indicated that the 6-strain community firstly adapted to bioleaching environment, dissolved the chalcopyrite rapidly and maintained an efficient work until late stage. Transcriptome profiles of the 6-strain community at 6th and 30th day during bioleaching process were investigated by RNA-seq. Comparative transcriptomics identified 226 and 737 significantly up-regulated genes at early and late stage, respectively. Gene annotation results revealed that microorganisms adapted to the oligotrophic environment by enhancing cell proliferation, catalytic activation and binding action to maintain their life activities at early stage, and genes related to signal transduction, localization and transporter were highly expressed as an effective response to the stressful late stage. A graphical representation was presented to show how microorganisms adapted and resisted to the extreme environment by their inner functional properties and promoted the bioleaching efficiency.
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Affiliation(s)
- Liyuan Ma
- School of Environmental Studies, China University of Geosciences, Wuhan 430074, China; Key Laboratory of Biometallurgy of Ministry of Education, Central South University, Changsha 410083, China.
| | - Hongmei Wang
- School of Environmental Studies, China University of Geosciences, Wuhan 430074, China
| | - Jiangjun Wu
- School of Environmental Studies, China University of Geosciences, Wuhan 430074, China
| | - Yuguang Wang
- Key Laboratory of Marine Biogenetic Resources, Third Institute of Oceanography, State Oceanic Administration, Xiamen 361005, China
| | - Du Zhang
- Key Laboratory of Biometallurgy of Ministry of Education, Central South University, Changsha 410083, China
| | - Xueduan Liu
- Key Laboratory of Biometallurgy of Ministry of Education, Central South University, Changsha 410083, China
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16
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Straub CT, Counts JA, Nguyen DMN, Wu CH, Zeldes BM, Crosby JR, Conway JM, Otten JK, Lipscomb GL, Schut GJ, Adams MWW, Kelly RM. Biotechnology of extremely thermophilic archaea. FEMS Microbiol Rev 2018; 42:543-578. [PMID: 29945179 DOI: 10.1093/femsre/fuy012] [Citation(s) in RCA: 53] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2018] [Accepted: 06/23/2018] [Indexed: 12/26/2022] Open
Abstract
Although the extremely thermophilic archaea (Topt ≥ 70°C) may be the most primitive extant forms of life, they have been studied to a limited extent relative to mesophilic microorganisms. Many of these organisms have unique biochemical and physiological characteristics with important biotechnological implications. These include methanogens that generate methane, fermentative anaerobes that produce hydrogen gas with high efficiency, and acidophiles that can mobilize base, precious and strategic metals from mineral ores. Extremely thermophilic archaea have also been a valuable source of thermoactive, thermostable biocatalysts, but their use as cellular systems has been limited because of the general lack of facile genetics tools. This situation has changed recently, however, thereby providing an important avenue for understanding their metabolic and physiological details and also opening up opportunities for metabolic engineering efforts. Along these lines, extremely thermophilic archaea have recently been engineered to produce a variety of alcohols and industrial chemicals, in some cases incorporating CO2 into the final product. There are barriers and challenges to these organisms reaching their full potential as industrial microorganisms but, if these can be overcome, a new dimension for biotechnology will be forthcoming that strategically exploits biology at high temperatures.
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Affiliation(s)
- Christopher T Straub
- Department of Chemical and Biomolecular Engineering North Carolina State University, Raleigh, NC 27695-7905, USA
| | - James A Counts
- Department of Chemical and Biomolecular Engineering North Carolina State University, Raleigh, NC 27695-7905, USA
| | - Diep M N Nguyen
- Department of Biochemistry and Molecular Biology University of Georgia, Athens, GA 30602, USA
| | - Chang-Hao Wu
- Department of Biochemistry and Molecular Biology University of Georgia, Athens, GA 30602, USA
| | - Benjamin M Zeldes
- Department of Chemical and Biomolecular Engineering North Carolina State University, Raleigh, NC 27695-7905, USA
| | - James R Crosby
- Department of Chemical and Biomolecular Engineering North Carolina State University, Raleigh, NC 27695-7905, USA
| | - Jonathan M Conway
- Department of Chemical and Biomolecular Engineering North Carolina State University, Raleigh, NC 27695-7905, USA
| | - Jonathan K Otten
- Department of Chemical and Biomolecular Engineering North Carolina State University, Raleigh, NC 27695-7905, USA
| | - Gina L Lipscomb
- Department of Biochemistry and Molecular Biology University of Georgia, Athens, GA 30602, USA
| | - Gerrit J Schut
- Department of Biochemistry and Molecular Biology University of Georgia, Athens, GA 30602, USA
| | - Michael W W Adams
- Department of Biochemistry and Molecular Biology University of Georgia, Athens, GA 30602, USA
| | - Robert M Kelly
- Department of Chemical and Biomolecular Engineering North Carolina State University, Raleigh, NC 27695-7905, USA
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17
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Calditol-linked membrane lipids are required for acid tolerance in Sulfolobus acidocaldarius. Proc Natl Acad Sci U S A 2018; 115:12932-12937. [PMID: 30518563 DOI: 10.1073/pnas.1814048115] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Archaea have many unique physiological features of which the lipid composition of their cellular membranes is the most striking. Archaeal ether-linked isoprenoidal membranes can occur as bilayers or monolayers, possess diverse polar head groups, and a multiplicity of ring structures in the isoprenoidal cores. These lipid structures are proposed to provide protection from the extreme temperature, pH, salinity, and nutrient-starved conditions that many archaea inhabit. However, many questions remain regarding the synthesis and physiological role of some of the more complex archaeal lipids. In this study, we identify a radical S-adenosylmethionine (SAM) protein in Sulfolobus acidocaldarius required for the synthesis of a unique cyclopentyl head group, known as calditol. Calditol-linked glycerol dibiphytanyl glycerol tetraethers (GDGTs) are membrane spanning lipids in which calditol is ether bonded to the glycerol backbone and whose production is restricted to a subset of thermoacidophilic archaea of the Sulfolobales order within the Crenarchaeota phylum. Several studies have focused on the enzymatic mechanism for the synthesis of the calditol moiety, but to date no protein that catalyzes this reaction has been discovered. Phylogenetic analyses of this putative calditol synthase (Cds) reveal the genetic potential for calditol-GDGT synthesis in phyla other than the Crenarchaeota, including the Korarchaeota and Marsarchaeota. In addition, we identify Cds homologs in metagenomes predominantly from acidic ecosystems. Finally, we demonstrate that deletion of calditol synthesis renders S. acidocaldarius sensitive to extremely low pH, indicating that calditol plays a critical role in protecting archaeal cells from acidic stress.
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18
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Nonmutational mechanism of inheritance in the Archaeon Sulfolobus solfataricus. Proc Natl Acad Sci U S A 2018; 115:12271-12276. [PMID: 30425171 DOI: 10.1073/pnas.1808221115] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Epigenetic phenomena have not yet been reported in archaea, which are presumed to use a classical genetic process of heritability. Here, analysis of independent lineages of Sulfolobus solfataricus evolved for enhanced fitness implicated a non-Mendelian basis for trait inheritance. The evolved strains, called super acid-resistant Crenarchaeota (SARC), acquired traits of extreme acid resistance and genome stability relative to their wild-type parental lines. Acid resistance was heritable because it was retained regardless of extensive passage without selection. Despite the hereditary pattern, in one strain, it was impossible for these SARC traits to result from mutation because its resequenced genome had no mutation. All strains also had conserved, heritable transcriptomes implicated in acid resistance. In addition, they had improved genome stability with absent or greatly decreased mutation and transposition relative to a passaged control. A mechanism that would confer these traits without DNA sequence alteration could involve posttranslationally modified archaeal chromatin proteins. To test this idea, homologous recombination with isogenic DNA was used to perturb native chromatin structure. Recombination at up-regulated loci from the heritable SARC transcriptome reduced acid resistance and gene expression in the majority of recombinants. In contrast, recombination at a control locus that was not part of the heritable transcriptome changed neither acid resistance nor gene expression. Variation in the amount of phenotypic and expression changes across individuals was consistent with Rad54-dependent chromatin remodeling that dictated crossover location and branch migration. These data support an epigenetic model implicating chromatin structure as a contributor to heritable traits.
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19
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Power JF, Carere CR, Lee CK, Wakerley GLJ, Evans DW, Button M, White D, Climo MD, Hinze AM, Morgan XC, McDonald IR, Cary SC, Stott MB. Microbial biogeography of 925 geothermal springs in New Zealand. Nat Commun 2018; 9:2876. [PMID: 30038374 PMCID: PMC6056493 DOI: 10.1038/s41467-018-05020-y] [Citation(s) in RCA: 101] [Impact Index Per Article: 16.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2018] [Accepted: 06/08/2018] [Indexed: 01/19/2023] Open
Abstract
Geothermal springs are model ecosystems to investigate microbial biogeography as they represent discrete, relatively homogenous habitats, are distributed across multiple geographical scales, span broad geochemical gradients, and have reduced metazoan interactions. Here, we report the largest known consolidated study of geothermal ecosystems to determine factors that influence biogeographical patterns. We measured bacterial and archaeal community composition, 46 physicochemical parameters, and metadata from 925 geothermal springs across New Zealand (13.9–100.6 °C and pH < 1–9.7). We determined that diversity is primarily influenced by pH at temperatures <70 °C; with temperature only having a significant effect for values >70 °C. Further, community dissimilarity increases with geographic distance, with niche selection driving assembly at a localised scale. Surprisingly, two genera (Venenivibrio and Acidithiobacillus) dominated in both average relative abundance (11.2% and 11.1%, respectively) and prevalence (74.2% and 62.9%, respectively). These findings provide an unprecedented insight into ecological behaviour in geothermal springs, and a foundation to improve the characterisation of microbial biogeographical processes. Power et al. catalogue the microbial biodiversity and physicochemistry of around 1000 hotsprings across New Zealand, providing insights into the ecological conditions that drive community assembly in these ecosystems.
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Affiliation(s)
- Jean F Power
- Geomicrobiology Research Group, Department of Geothermal Sciences, GNS Science, Taupō, 3384, New Zealand.,Thermophile Research Unit, School of Science, University of Waikato, Hamilton, 3240, New Zealand
| | - Carlo R Carere
- Geomicrobiology Research Group, Department of Geothermal Sciences, GNS Science, Taupō, 3384, New Zealand.,Department of Chemical and Process Engineering, University of Canterbury, Christchurch, 8140, New Zealand
| | - Charles K Lee
- Thermophile Research Unit, School of Science, University of Waikato, Hamilton, 3240, New Zealand
| | - Georgia L J Wakerley
- Thermophile Research Unit, School of Science, University of Waikato, Hamilton, 3240, New Zealand
| | - David W Evans
- Geomicrobiology Research Group, Department of Geothermal Sciences, GNS Science, Taupō, 3384, New Zealand
| | - Mathew Button
- Department of Computer Science, University of Waikato, Hamilton, 3240, New Zealand
| | - Duncan White
- Wairakei Research Centre, GNS Science, Taupō, 3384, New Zealand
| | - Melissa D Climo
- Wairakei Research Centre, GNS Science, Taupō, 3384, New Zealand.,School of Biological Sciences, University of Canterbury, Christchurch, 8140, New Zealand
| | - Annika M Hinze
- Department of Computer Science, University of Waikato, Hamilton, 3240, New Zealand
| | - Xochitl C Morgan
- Department of Microbiology and Immunology, University of Otago, Dunedin, 9054, New Zealand
| | - Ian R McDonald
- Thermophile Research Unit, School of Science, University of Waikato, Hamilton, 3240, New Zealand
| | - S Craig Cary
- Thermophile Research Unit, School of Science, University of Waikato, Hamilton, 3240, New Zealand.
| | - Matthew B Stott
- Geomicrobiology Research Group, Department of Geothermal Sciences, GNS Science, Taupō, 3384, New Zealand. .,School of Biological Sciences, University of Canterbury, Christchurch, 8140, New Zealand.
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20
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McCarthy S, Ai C, Blum P. Enhancement of Metallosphaera sedula Bioleaching by Targeted Recombination and Adaptive Laboratory Evolution. ADVANCES IN APPLIED MICROBIOLOGY 2018; 104:135-165. [PMID: 30143251 DOI: 10.1016/bs.aambs.2018.03.002] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
Thermophilic and lithoautotrophic archaea such as Metallosphaera sedula occupy acidic, metal-rich environments and are used in biomining processes. Biotechnological approaches could accelerate these processes and improve metal recovery by biomining organisms, but systems for genetic manipulation in these organisms are currently lacking. To gain a better understanding of the interplay between metal resistance, autotrophy, and lithotrophic metabolism, a genetic system was developed for M. sedula and used to evaluate parameters governing the efficiency of copper bioleaching. Additionally, adaptive laboratory evolution was used to select for naturally evolved M. sedula cell lines with desirable phenotypes for biomining, and these adapted cell lines were shown to have increased bioleaching capacity and efficiency. Genomic methods were used to analyze mutations that led to resistance in the experimentally evolved cell lines, while transcriptomics was used to examine changes in stress-inducible gene expression specific to the environmental conditions.
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Affiliation(s)
- Samuel McCarthy
- School of Biological Sciences, University of Nebraska-Lincoln, Lincoln, NE, United States
| | - Chenbing Ai
- School of Biological Sciences, University of Nebraska-Lincoln, Lincoln, NE, United States
| | - Paul Blum
- School of Biological Sciences, University of Nebraska-Lincoln, Lincoln, NE, United States.
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21
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Gumulya Y, Boxall NJ, Khaleque HN, Santala V, Carlson RP, Kaksonen AH. In a quest for engineering acidophiles for biomining applications: challenges and opportunities. Genes (Basel) 2018; 9:E116. [PMID: 29466321 PMCID: PMC5852612 DOI: 10.3390/genes9020116] [Citation(s) in RCA: 45] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2018] [Revised: 02/16/2018] [Accepted: 02/16/2018] [Indexed: 12/27/2022] Open
Abstract
Biomining with acidophilic microorganisms has been used at commercial scale for the extraction of metals from various sulfide ores. With metal demand and energy prices on the rise and the concurrent decline in quality and availability of mineral resources, there is an increasing interest in applying biomining technology, in particular for leaching metals from low grade minerals and wastes. However, bioprocessing is often hampered by the presence of inhibitory compounds that originate from complex ores. Synthetic biology could provide tools to improve the tolerance of biomining microbes to various stress factors that are present in biomining environments, which would ultimately increase bioleaching efficiency. This paper reviews the state-of-the-art tools to genetically modify acidophilic biomining microorganisms and the limitations of these tools. The first part of this review discusses resilience pathways that can be engineered in acidophiles to enhance their robustness and tolerance in harsh environments that prevail in bioleaching. The second part of the paper reviews the efforts that have been carried out towards engineering robust microorganisms and developing metabolic modelling tools. Novel synthetic biology tools have the potential to transform the biomining industry and facilitate the extraction of value from ores and wastes that cannot be processed with existing biomining microorganisms.
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Affiliation(s)
- Yosephine Gumulya
- Commonwealth Scientific and Industrial Research Organisation (CSIRO), Floreat WA 6014, Australia.
| | - Naomi J Boxall
- Commonwealth Scientific and Industrial Research Organisation (CSIRO), Floreat WA 6014, Australia.
| | - Himel N Khaleque
- Commonwealth Scientific and Industrial Research Organisation (CSIRO), Floreat WA 6014, Australia.
| | - Ville Santala
- Laboratory of Chemistry and Bioengineering, Tampere University of Technology (TUT), Tampere, 33101, Finland.
| | - Ross P Carlson
- Department of Chemical and Biological Engineering, Montana State University (MSU), Bozeman, MT 59717, USA.
| | - Anna H Kaksonen
- Commonwealth Scientific and Industrial Research Organisation (CSIRO), Floreat WA 6014, Australia.
- School of Pathology and Laboratory Medicine, University of Western Australia, Crawley, WA 6009, Australia.
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22
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Evolution of copper arsenate resistance for enhanced enargite bioleaching using the extreme thermoacidophile Metallosphaera sedula. J Ind Microbiol Biotechnol 2017; 44:1613-1625. [DOI: 10.1007/s10295-017-1973-5] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2017] [Accepted: 07/26/2017] [Indexed: 10/19/2022]
Abstract
Abstract
Adaptive laboratory evolution (ALE) was employed to isolate arsenate and copper cross-resistant strains, from the copper-resistant M. sedula CuR1. The evolved strains, M. sedula ARS50-1 and M. sedula ARS50-2, contained 12 and 13 additional mutations, respectively, relative to M. sedula CuR1. Bioleaching capacity of a defined consortium (consisting of a naturally occurring strain and a genetically engineered copper sensitive strain) was increased by introduction of M. sedula ARS50-2, with 5.31 and 26.29% more copper recovered from enargite at a pulp density (PD) of 1 and 3% (w/v), respectively. M. sedula ARS50-2 arose as the predominant species and modulated the proportions of the other two strains after it had been introduced. Collectively, the higher Cu2+ resistance trait of M. sedula ARS50-2 resulted in a modulated microbial community structure, and consolidating enargite bioleaching especially at elevated PD.
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23
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Geobiological feedbacks and the evolution of thermoacidophiles. ISME JOURNAL 2017; 12:225-236. [PMID: 29028004 PMCID: PMC5739016 DOI: 10.1038/ismej.2017.162] [Citation(s) in RCA: 47] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/09/2017] [Revised: 07/27/2017] [Accepted: 08/28/2017] [Indexed: 12/14/2022]
Abstract
Oxygen-dependent microbial oxidation of sulfur compounds leads to the acidification of natural waters. How acidophiles and their acidic habitats evolved, however, is largely unknown. Using 16S rRNA gene abundance and composition data from 72 hot springs in Yellowstone National Park, Wyoming, we show that hyperacidic (pH<3.0) hydrothermal ecosystems are dominated by a limited number of archaeal lineages with an inferred ability to respire O2. Phylogenomic analyses of 584 existing archaeal genomes revealed that hyperacidophiles evolved independently multiple times within the Archaea, each coincident with the emergence of the ability to respire O2, and that these events likely occurred in the recent evolutionary past. Comparative genomic analyses indicated that archaeal thermoacidophiles from independent lineages are enriched in similar protein-coding genes, consistent with convergent evolution aided by horizontal gene transfer. Because the generation of acidic environments and their successful habitation characteristically require O2, these results suggest that thermoacidophilic Archaea and the acidity of their habitats co-evolved after the evolution of oxygenic photosynthesis. Moreover, it is likely that dissolved O2 concentrations in thermal waters likely did not reach levels capable of sustaining aerobic thermoacidophiles and their acidifying activity until ~0.8 Ga, when present day atmospheric levels were reached, a time period that is supported by our estimation of divergence times for archaeal thermoacidophilic clades.
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24
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Increased acid resistance of the archaeon, Metallosphaera sedula by adaptive laboratory evolution. ACTA ACUST UNITED AC 2016; 43:1455-65. [DOI: 10.1007/s10295-016-1812-0] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2016] [Accepted: 07/30/2016] [Indexed: 10/21/2022]
Abstract
Abstract
Extremely thermoacidophilic members of the Archaea such as the lithoautotroph, Metallosphaera sedula, are among the most acid resistant forms of life and are of great relevance in bioleaching. Here, adaptive laboratory evolution was used to enhance the acid resistance of this organism while genomics and transcriptomics were used in an effort to understand the molecular basis for this trait. Unlike the parental strain, the evolved derivative, M. sedula SARC-M1, grew well at pH of 0.90. Enargite (Cu3AsS4) bioleaching conducted at pH 1.20 demonstrated SARC-M1 leached 23.78 % more copper relative to the parental strain. Genome re-sequencing identified two mutations in SARC-M1 including a nonsynonymous mutation in Msed_0408 (an amino acid permease) and a deletion in pseudogene Msed_1517. Transcriptomic studies by RNA-seq of wild type and evolved strains at various low pH values demonstrated there was enhanced expression of genes in M. sedula SARC-M1 encoding membrane complexes and enzymes that extrude protons or that catalyze proton-consuming reactions. In addition, M. sedula SARC-M1 exhibited reduced expression of genes encoding enzymes that catalyze proton-generating reactions. These unique genomic and transcriptomic features support a model for increased acid resistance arising from enhanced control over cytoplasmic pH.
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