Adaptation at the Extremes of Life: Experimental Evolution with the Extremophile Archaeon Sulfolobus acidocaldarius

Published: June 14, 2024

doi:

Zahraa Al-Baqsami*^1,2,3, Rebecca Lowry Palmer*^1,3, Gwyneth Darwent, Andrew J. McBain, Christopher G. Knight, Danna R. Gifford

¹Division of Evolution, Infection and Genomics, School of Biological Sciences,The University of Manchester, ²Division of Pharmacy and Optometry, School of Health Sciences,The University of Manchester, ³Department of Earth and Environmental Sciences, School of Natural Sciences,The University of Manchester

Summary

Here, we present an experimental evolution protocol for adaptation in thermophiles utilizing low-cost, energy-efficient bench-top thermomixers as incubators. The technique is demonstrated through the characterization of temperature adaptation in Sulfolobus acidocaldarius, an archaeon with an optimal growth temperature of 75 °C.

Abstract

The archaeon Sulfolobus acidocaldarius has emerged as a promising thermophilic model system. Investigating how thermophiles adapt to changing temperatures is a key requirement, not only for understanding fundamental evolutionary processes but also for developing S. acidocaldarius as a chassis for bioengineering. One major obstacle to conducting experimental evolution with thermophiles is the expense of equipment maintenance and energy usage of traditional incubators for high-temperature growth. To address this challenge, a comprehensive experimental protocol for conducting experimental evolution in S. acidocaldarius is presented, utilizing low-cost and energy-efficient bench-top thermomixers. The protocol involves a batch culture technique with relatively small volumes (1.5 mL), enabling tracking of adaptation in multiple independent lineages. This method is easily scalable through the use of additional thermomixers. Such an approach increases the accessibility of S. acidocaldarius as a model system by reducing both initial investment and ongoing costs associated with experimental investigations. Moreover, the technique is transferable to other microbial systems for exploring adaptation to diverse environmental conditions.

Introduction

Early life on Earth may have originated in extreme environments, such as hydrothermal vents, which are characterized by extremely high temperatures and acidity¹. Microbes continue to inhabit extreme environments, including hot springs and volcanic solfatara. Characterizing the evolutionary dynamics that occur under these extreme conditions may shed light on the specialized physiological processes that enable survival under these conditions. This may have wide-ranging implications, from our understanding of the origins of biological diversity to the development of novel high-temperature enzymes with biotechnological applications.

The understanding of microbial evolutionary dynamics in extreme environments remains limited despite its critical importance. In contrast, a significant body of knowledge about evolution in mesophilic environments has been acquired through the application of a technique known as experimental evolution. Experimental evolution involves observing evolutionary change under laboratory conditions²^,³^,⁴^,⁵. Often, this involves a defined change environment (e.g., temperature, salinity, introduction of a toxin or a competitor organism)⁷^,⁸^,⁹. When combined with whole-genome sequencing, experimental evolution has enabled us to test key aspects of evolutionary processes, including parallelism, repeatability, and the genomic basis for adaptation. However, to date, the bulk of experimental evolution has been performed with mesophilic microbes (including bacteria, fungi, and viruses²^,³^,⁴^,⁵, but largely excluding archaea). A method for experimental evolution applicable to thermophilic microbes would enable us to better understand how they evolve and contribute to a more comprehensive understanding of evolution. This has potentially wide-ranging implications, from deciphering the origins of thermophilic life on Earth to biotechnological applications involving 'extremozymes' used in high-temperature bioprocesses¹⁰ and astrobiological research¹¹.

The archaeon Sulfolobus acidocaldarius is an ideal candidate as a model organism for developing experimental evolution techniques for thermophiles. S. acidocaldarius reproduces aerobically, with an optimal growth temperature at 75 °C (range 55 °C to 85 °C) and high acidity (pH 2-3)⁴^,⁶^,¹²^,¹³^,¹⁴. Remarkably, despite its extreme growth conditions, S. acidocaldarius maintains population densities and mutation rates comparable to mesophiles⁷^,¹⁵^,¹⁶^,¹⁷^,¹⁸. In addition, it possesses a relatively small, well-annotated genome (strain DSM639: 2.2 Mb, 36.7% GC, 2,347 genes)¹²; S. acidocaldarius also benefits from robust genome engineering tools, allowing for a direct assessment of the evolutionary process through targeted gene knockouts¹⁹. A notable example of this is the availability of genetically modified strains of S. acidocaldarius, such as the uracil auxotrophic strains of MW001¹⁹ and SK-1²⁰, which can serve as selectable markers.

There are significant challenges with conducting experimental evolution with thermophiles like S. acidocaldarius. Extended incubation at high temperatures required for these studies imposes considerable evaporation for both liquid and solid culturing techniques. Extended operation at high temperatures can also damage the traditional shaking incubators that are commonly used in experimental evolution in liquid media. Exploring multiple temperatures necessitates a substantial financial investment for acquiring and maintaining several incubators. Furthermore, the high energy consumption required raises significant environmental and financial concerns.

This work introduces a method to address the challenges encountered in performing experimental evolution with thermophiles like S. acidocaldarius. Building upon a technique developed by Baes et al. for investigating heat shock response¹⁴^,²¹, the method developed here utilizes bench-top thermomixers for consistent and reliable high-temperature incubation. Its scalability allows for the simultaneous assessment of multiple temperature treatments, with reduced costs in acquiring additional incubation equipment. This enhances experimental efficiency, enabling robust statistical analysis and extensive investigation of factors influencing evolutionary dynamics in thermophiles²². Moreover, this approach significantly reduces the financial initial investment and energy consumption compared to traditional incubators, offering a more sustainable and environmentally friendly alternative.

Our method lays the groundwork for experimentally investigating evolutionary dynamics in environments characterized by extreme temperatures, which may have played a key role during the early stages of the diversification of life on Earth. Thermophilic organisms have unique properties, but their extreme growth conditions and specialized requirements have often limited their accessibility as a model system. Overcoming these barriers not only expands research opportunities for investigating evolutionary dynamics but also enhances the broader utility of thermophiles as model systems in scientific research.

Protocol

1. Preparation of S. acidocaldarius growth medium (BBM+) NOTE: To cultivate S. acidocaldarius, this protocol uses Basal Brock Medium (BBM+)23. This is prepared by first combining the inorganic stock solutions outlined below to create BBM−, which may be prepared in advance. BBM+ is then prepared as needed by adding the organic stock solutions to BBM−. Stock solution recip…

Representative Results

Growth curve measurements Growth curves for S. acidocaldarius DSM639 are shown in Figure 3A. Growth was found to be similar when comparing incubation using thermomixers with that in conventional incubators. Average growth rate parameters were estimated by fitting a logistic curve to each replicated growth curve and calculating the mean and standard error. Times to mid-exponential phase on the thermomixer and incubator were 27.2 h ± 1.1 h and 31.1 h ±…

Discussion

This work has developed an experimental evolution protocol for thermophiles, here tailored for the archaeon S. acidocaldarius, but adaptable to other microbes with high-temperature growth requirements. This protocol builds on techniques initially designed for mesophilic bacteria but is specifically modified to overcome the technical challenges associated with high-temperature aerobic growth²^,⁴^,⁵^,<sup class="x…

Disclosures

The authors have nothing to disclose.

Acknowledgements

The authors thank Prof SV Albers (University of Freiburg), Prof Eveline Peeters (Vrije Universiteit Brussel), and Dr Rani Baes (Vrije Universiteit Brussel) for advice and the S. acidocaldarius DSM639 strain. This work was funded by a Royal Society Research Grant (awarded to DRG: RGS\R1\231308), a UKRI-NERC "Exploring the Frontiers" Research Grant (awarded to DRG and CGK: NE/X012662/1), and a Kuwait University PhD scholarship (awarded to ZA).

Materials

0.22 μm syringe-driven membrane filters	StarLab	E4780-1226	For filter sterilising media components that cannot be autoclaved.
1 μL inoculation loops	Greiner	731161, 731165, or 731101	For inoculating cultures. Other loops can be used.
1000 μL pipette tips	StarLab	S1111-6811	Other pipette tips can be used.
2 mL microcentrifuge tubes	StarLab	S1620-2700	For culturing S. acidocaldarius in thermomixers.
200 μL pipette tips	StarLab	S1111-0816	Other pipette tips can be used.
50 mL polystyrene tubes with conical bottom	Corning	430828 or 430829	Other tubes may be used. Check performance at 75 °C. Tubes with plug seal caps may not allow sufficient aeration; check before using.
50 mL syringe	BD plastipak	300865	For use with syringe-driven filters.
96 well microtitre plates (non-treated, flat bottom)	Nunc	260860	For measuring OD at 600 nm in spectrophotometer.
Adjustable width multichannel pipette	Pipet-Lite	LA8-300XLS	Optional, but saves time when transferring between microcentrifuge and 96 well plates.
Ammonium sulfate ((NH₄)₂SO₄)	Millipore	168355	For Brock stock solution I.
Autoclave	Priorclave	B60-SMART or SV100-BASE	Other autoclaves can also be used.
Breathe-EASY gas permeable sealing membrane	Sigma-Aldrich	Z763624-100EA	Cut to size to use on pierced microcentrifuge tubes. If substituting other gas permeable memrbanes, ensure performance is adequate at 75 °C
Calcium chloride dihydrate (CaCl₂·2H₂O)	Sigma-Aldrich	C3306	For Brock stock solution I.
CELLSTAR Six well plates (suspension/non-treated)	Greiner	M9062	Other manufacturers' six well plates can likely be substituted. Check performance at high temperatures.
Cobalt(II) sulfate heptahydrate (CoSO₄·7H₂O)	Supelco	1025560100	For Trace element stock solution.
Copper(II) chloride dihydrate (CuCl₂·2H₂O)	Sigma-Aldrich	307483	For Trace element stock solution.
D-(+)-glucose anhydrous (C₆H₁₂O₆)	Thermo Scientific Chemicals	11462858	Other pentose and hexose sugars may also be used (e.g. D-xylose, D-arabinose). Glucose is not a preferred carbon source for S. acidocaldarius (SV Albers, personal communication)
Double-distilled water (ddH₂O)
Gelrite	Duchefa Biochemie	G1101.1000	Gelrite (gellan gum) is used in place of agar to make solid media due to its higher melting point.
Glass 100 mm Petri dishes	Brand	BR455742	Glass Petri dishes are used because most standard polystyrene 90 mm Petri dishes deform at 75 °C (brand-dependent). Alternatively, six well plates can be used as these do not deform at high temperatures.
Incubator	New Brunswick	Innnova 42R	Other incubators can also be used. Check the operating temperature for equipment prior to purchase/use, as many incubators are not capable of temperatures higher than 65°C.
Iron(III) chloride hexahydrate (FeCl₃·6H₂O)	Supelco	103943	For Fe Stock Solution
Magnesium sulfate heptahydrate (Epsom salt) (MgSO₄·7H₂O)	Sigma-Aldrich	230391	For Brock stock solution I.
Manganese(II) chloride tetrahydrate (MnCl₂·4H₂O)	Sigma-Aldrich	SIALM5005-100G	For Trace element stock solution.
Mini Smart Wi-Fi Socket, Energy Monitoring	Tapo	Tapo P110	To monitor energy consumtion
N-Z-Amine A – Casein enzymatic hydrolysate	Sigma-Aldrich	C0626-500G	N-Z-Amine-A is used as a source of amino acids.
Paper clip (or other sturdy wire)	none	none	For piercing 2 mL microcentrifuge tubes.
Potassium dihydrogen phosphate (Monopotassium phosphate) (KH₂PO₄)	Sigma-Aldrich	P0662	For Brock stock solution I.
Promega Wizard Genomic DNA Purification Kit	Promega	A1120	Optional, to extract genomic DNA in the lab
Sodium molybdate dihydrate (Na₂MoO₄·2H₂O)	Sigma-Aldrich	M1651-100G	For Trace element stock solution.
Sodium tetraborate decahydrate (Borax) (Na₂B₄O₇·10H₂O)	Sigma-Aldrich	S9640	For Trace element stock solution.
Spectrophotometer	BMG	SPECTROstar OMEGA	For measuring OD at 600 nm. Other spectrophotometers that can read OD at 600 nm can be used.
Sulfuric acid (Diluted in a 1:1 ratio with water) (H₂SO₄)	Thermo Scientific Chemicals	11337588	Used to adjust pH of Brock stock solution II/III to a final pH of 2–3.
Thermomixer	DLab	HM100-Pro	Other thermomixers can also be used; key consideration is the ability to maintain 65–75 °C temperatures and 400 RPM
Uracil (C₄H₄N₂O₂)	Sigma-Aldrich	U0750	Deletion of pyrE is a common genetic marker used in S. acidocaldarius. Deletion strains must be supplemented with uracil for growth. Supplementation is not strictly required for the DSM639 wild-type strain, but is included here as future experiments may involve deletion strains.
Vanadyl sulfate dihydrate (VOSO₄·2H₂O)	Sigma-Aldrich	204862	For Trace element stock solution.
Zinc sulfate heptahydrate (ZnSO₄·7H₂O)	Sigma-Aldrich	221376	For Trace element stock solution.

References

Nisbet, E. G., Sleep, N. H. The habitat and nature of early life. Nature. 409 (6823), 1083-1091 (2001).
Buckling, A., Craig Maclean, R., Brockhurst, M. A., Colegrave, N. The Beagle in a bottle. Nature. 457 (7231), 824-829 (2009).
Lenski, R. E. Experimental evolution and the dynamics of adaptation and genome evolution in microbial populations. ISME J. 11 (10), 2181-2194 (2017).
McDonald, M. J. Microbial experimental evolution – a proving ground for evolutionary theory and a tool for discovery. EMBO Rep. 20 (8), e46992 (2019).
Van Den Bergh, B., Swings, T., Fauvart, M., Michiels, J. Experimental design, population dynamics, and diversity in microbial experimental evolution. Microbiol Mol Biol Rev. 82 (3), e00008-e00018 (2018).
McCarthy, S., et al. Expanding the limits of thermoacidophily in the archaeon Sulfolobus solfataricus by adaptive evolution. Appl Environ Microbiol. 82 (3), 857-867 (2016).
Grogan, D. W. The question of DNA repair in hyperthermophilic archaea. Trends Microbiol. 8 (4), 180-185 (2000).
Whitaker, R. J. Population dynamics through the lens of extreme environments. Rev Mineral Geochem. 59 (1), 259-277 (2005).
Peeters, E., Thia-Toong, T. -. L., Gigot, D., Maes, D., Charlier, D. Ss-LrpB, a novel Lrp-like regulator of Sulfolobus solfataricus P2, binds cooperatively to three conserved targets in its own control region: Ss-LrpB-operator interactions for autoregulation. Mol Microbiol. 54 (2), 321-336 (2004).
Quehenberger, J., Shen, L., Albers, S. -. V., Siebers, B., Spadiut, O. Sulfolobus – A potential key organism in future biotechnology. Front Microbiol. 8, 2474 (2017).
Schultz, J., Dos Santos, A., Patel, N., Rosado, A. S. Life on the edge: Bioprospecting extremophiles for astrobiology. J Indian Inst Sci. 103 (3), 721-737 (2023).
Chen, L., et al. The genome of Sulfolobus acidocaldarius, a model organism of the Crenarchaeota. J Bacteriol. 187 (14), 4992-4999 (2005).
Rastädter, K., Wurm, D. J., Spadiut, O., Quehenberger, J. Physiological characterization of Sulfolobus acidocaldarius in a controlled bioreactor environment. Int J Environ Res Public Health. 18 (11), 5532 (2021).
Baes, R., Lemmens, L., Mignon, K., Carlier, M., Peeters, E. Defining heat shock response for the thermoacidophilic model crenarchaeon Sulfolobus acidocaldarius. Extremophiles. 24 (5), 681-692 (2020).
Grogan, D. W. Hyperthermophiles and the problem of DNA instability. Mol Microbiol. 28 (6), 1043-1049 (1998).
Grogan, D. W. Understanding DNA repair in hyperthermophilic archaea: Persistent gaps and other reasons to focus on the fork. Archaea. 2015, 942605 (2015).
Drake, J. W. Avoiding dangerous missense: Thermophiles display especially low mutation rates. PLoS Genet. 5 (6), e1000520 (2009).
Grogan, D. W., Carver, G. T., Drake, J. W. Genetic fidelity under harsh conditions: Analysis of spontaneous mutation in the thermoacidophilic archaeon Sulfolobus acidocaldarius. Proc Natl Acad Sci U S A. 98 (14), 7928-7933 (2001).
Wagner, M., et al. Versatile genetic tool box for the Crenarchaeote Sulfolobus acidocaldarius. Front Microbiol. 3, 214 (2012).
Suzuki, S., Kurosawa, N. Disruption of the gene encoding restriction endonuclease SuaI and development of a host-vector system for the thermoacidophilic archaeon Sulfolobus acidocaldarius. Extremophiles. 20 (2), 139-148 (2016).
Baes, R., et al. Transcriptional and translational dynamics underlying heat shock response in the thermophilic crenarchaeon Sulfolobus acidocaldarius. mBio. 14 (5), e0359322 (2023).
González, A. G., Pérez Y Terrón, R. Importance of extremophilic microorganisms in biogeochemical cycles. GSC Adv Res Rev. 9 (1), 082-093 (2021).
Brock, T. D., Brock, K. M., Belly, R. T., Weiss, R. L. Sulfolobus: A new genus of sulfur-oxidizing bacteria living at low pH and high temperature. Arch Mikrobiol. 84 (1), 54-68 (1972).
Lenski, R. E., Rose, M. R., Simpson, S. C., Tadler, S. C. Long-term experimental evolution in Escherichia coli. I. Adaptation and divergence during 2,000 generations. Am Nat. 138 (6), 1315-1341 (1991).
. Exploring transcriptional and translational regulatory mechanisms of the heat shock response of Sulfolobus acidocaldarius. Master’s Thesis Available from: https://researchportal.vub.be/en/studentTheses/exploring-transcriptional-and-translational-regulatory-mechanisms (2018)
Wahl, L. M., Gerrish, P. J., Saika-Voivod, I. Evaluating the impact of population bottlenecks in experimental evolution. Genetics. 162 (2), 961-971 (2002).
Bernander, R. The cell cycle of Sulfolobus. Mol Microbiol. 66 (3), 557-562 (2007).
Breslow, D. K., et al. A comprehensive strategy enabling high-resolution functional analysis of the yeast genome. Nat Methods. 5 (8), 711-718 (2008).
Lang, G. I., Botstein, D., Desai, M. M. Genetic variation and the fate of beneficial mutations in asexual populations. Genetics. 188 (3), 647-661 (2011).
Frenzel, E., Legebeke, J., Van Stralen, A., Van Kranenburg, R., Kuipers, O. P. In vivo selection of sfGFP variants with improved and reliable functionality in industrially important thermophilic bacteria. Biotechnol Biofuels. 11, 8 (2018).
Visone, V., et al. In vivo and in vitro protein imaging in thermophilic archaea by exploiting a novel protein tag. PLoS One. 12 (10), e0185791 (2017).
Campbell, B. C., Paez-Segala, M. G., Looger, L. L., Petsko, G. A., Liu, C. F. Chemically stable fluorescent proteins for advanced microscopy. Nat Methods. 19 (12), 1612-1621 (2022).