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Transcriptomic Analysis Reveals Common Adaptation Mechanisms Under Different Stresses for Moderately Piezophilic Bacteria

Abstract

Piezophiles, by the commonly accepted definition, grow faster under high hydrostatic pressure (HHP) than under ambient pressure and are believed to exist only in pressurized environments where life has adapted to HHP during evolution. However, recent findings suggest that piezophiles have developed a common adaptation strategy to cope with multiple types of stresses including HHP. These results raise a question on the ecological niches of piezophiles: are piezophiles restricted to habitats with HHP? In this study, we observed that the bacterial strains Sporosarcina psychrophila DSM 6497 and Lysinibacillus sphaericus LMG 22257, which were isolated from surface environments and then transferred under ambient pressure for half a century, possess moderately piezophilic characteristics with optimal growth pressures of 7 and 20 MPa, respectively. Their tolerance to HHP was further enhanced by MgCl2 supplementation under the highest tested pressure of 50 MPa. Transcriptomic analysis was performed to compare gene expression with and without MgCl2 supplementation under 50 MPa for S. psychrophila DSM 6497. Among 4390 genes or transcripts obtained, 915 differentially expressed genes (DEGs) were identified. These DEGs are primarily associated with the antioxidant defense system, intracellular compatible solute accumulation, and membrane lipid biosynthesis, which have been reported to be essential for cells to cope with HHP. These findings indicate no in situ pressure barrier for piezophile isolation, and cells may adopt a common adaptation strategy to cope with different stresses.

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References

  1. 1.

    Kato C, Nogi Y, Arakawa S (2008) Isolation, cultivation, and diversity of deep-sea piezophiles. In: Michiels C, Bartlett DH, Aersten A (eds) High-pressure microbiology. ASM, Washington, pp 203–217

    Google Scholar 

  2. 2.

    Yayanos AA, Dietz AS, Van Boxtel R (1979) Isolation of a deep-sea barophilic bacterium and some of its growth characteristics. Science 205:808–810. https://doi.org/10.1126/science.205.4408.808

    CAS  Article  PubMed  Google Scholar 

  3. 3.

    Zeng X, Birrien J-L, Fouquet Y, Cherkashov G, Jebbar M, Querellou J, Oger P, Cambon-Bonavita M-A, Xiao X, Prieur D (2009) Pyrococcus CH1, an obligate piezophilic hyperthermophile: extending the upper pressure-temperature limits for life. ISME J 3:873–876. https://doi.org/10.1038/ismej.2009.21

    CAS  Article  PubMed  Google Scholar 

  4. 4.

    Huber H, Thomm M, König H, Thies G, Stetter K (1982) Methanococcus thermolithotrophicus, a novel thermophilic lithotrophic methanogen. Arch Microbiol 132:47–50. https://doi.org/10.1007/bf00690816

    Article  Google Scholar 

  5. 5.

    Bernhardt G, Jaenicke R, Lüdemann HD, König H, Stetter KO (1988) High pressure enhances the growth rate of the thermophilic archaebacterium Methanococcus thermolithotrophicus without extending its temperature range. Appl Environ Microbiol 54:1258–1261. https://doi.org/10.1128/aem.54.5.1258-1261.1988

    CAS  Article  PubMed  PubMed Central  Google Scholar 

  6. 6.

    Li Y, Mandelco L, Wiegel J (1993) Isolation and characterization of a moderately thermophilic anaerobic alkaliphile, Clostridium paradoxum sp. nov. Int J Syst Evol Microbiol 43:450–460. https://doi.org/10.1099/00207713-43-3-450

    Article  Google Scholar 

  7. 7.

    Scoma A, Garrido-Amador P, Nielsen SD, Røy H, Kjeldsen KU (2019) The polyextremophilic acterium Clostridium paradoxum attains piezophilic traits by modulating its energy metabolism and cell membrane composition. Appl Environ Microbiol 85:e00802–e00819. https://doi.org/10.1128/aem.00802-19

    CAS  Article  PubMed  PubMed Central  Google Scholar 

  8. 8.

    Lauro FM, Eloe EA, Liverani N, Bertoloni G, Bartlett DH (2005) Conjugal vectors for cloning, expression, and insertional mutagenesis in Gram-negative bacteria. BioTechniques 38:708–712. https://doi.org/10.2144/05385bm06

    CAS  Article  PubMed  Google Scholar 

  9. 9.

    Chen Y, Wang F, Xu J, Mehmood MA, Xiao X (2011) Physiological and evolutionary studies of NAP systems in Shewanella piezotolerans WP3. ISME J 5:843–855. https://doi.org/10.1038/ismej.2010.182

    CAS  Article  PubMed  Google Scholar 

  10. 10.

    Macgregor RB (2002) The interactions of nucleic acids at elevated hydrostatic pressure. BBA- Protein Struct M 1595:266–276. https://doi.org/10.1016/s0167-4838(01)00349-1

    CAS  Article  Google Scholar 

  11. 11.

    Kato C, Qureshi MH, Horikoshi K (1999) Pressure response in deep-sea piezophilic bacteria. J Mol Microbiol Biotechnol 1:87–92

    CAS  PubMed  Google Scholar 

  12. 12.

    Gross M, Jaenicke R (1994) Proteins under pressure. Eur J Biochem 221:617–630. https://doi.org/10.1111/j.1432-1033.1994.tb18774.x

    CAS  Article  PubMed  Google Scholar 

  13. 13.

    Campanaro S, Vezzi A, Vitulo N, Lauro FM, D'Angelo M, Simonato F, Cestaro A, Malacrida G, Bertoloni G, Valle G, Bartlett DH (2005) Laterally transferred elements and high pressure adaptation in Photobacterium profundum strains. BMC Genomics 6:122. https://doi.org/10.1186/1471-2164-6-122

    CAS  Article  PubMed  PubMed Central  Google Scholar 

  14. 14.

    Wang F, Wang J, Jian H, Zhang B, Li S, Wang F, Zeng X, Gao L, Bartlett DH, Yu J, Hu S, Xiao X (2008) Environmental adaptation: genomic analysis of the piezotolerant and psychrotolerant deep-sea iron reducing bacterium Shewanella piezotolerans WP3. PLoS One 3:e1937. https://doi.org/10.1371/journal.pone.0001937

    CAS  Article  PubMed  PubMed Central  Google Scholar 

  15. 15.

    Winter R, Jeworrek C (2009) Effect of pressure on membranes. Soft Matter 5:3157–3173. https://doi.org/10.1039/B901690B

    CAS  Article  Google Scholar 

  16. 16.

    Zhang Y, Li X, Bartlett DH, Xiao X (2015) Current developments in marine microbiology: high-pressure biotechnology and the genetic engineering of piezophiles. Curr Opin Biotechnol 33:157–164. https://doi.org/10.1016/j.copbio.2015.02.013

    CAS  Article  PubMed  Google Scholar 

  17. 17.

    Ambily Nath IV, Loka Bharathi PA (2011) Diversity in transcripts and translational pattern of stress proteins in marine extremophiles. Extremophiles 15:129–153. https://doi.org/10.1007/s00792-010-0348-x

    CAS  Article  PubMed  Google Scholar 

  18. 18.

    Xie Z, Jian H, Jin Z, Xiao X (2018) Enhancing the adaptability of the deep-sea bacterium Shewanella piezotolerans WP3 to high pressure and low temperature by experimental evolution under H2O2 stress. Appl Environ Microbiol 84:e02342–e02317. https://doi.org/10.1128/aem.02342-17

    CAS  Article  PubMed  PubMed Central  Google Scholar 

  19. 19.

    Marquis RE, ZoBell CE (1971) Magnesium and calcium ions enhance barotolerance of Streptococci. Arch Microbiol 79:80–92. https://doi.org/10.1007/BF00412043

    CAS  Article  Google Scholar 

  20. 20.

    Landau J, Pope D (1980) Recent advances in the area of barotolerant protein synthesis in bacteria and implications concerning barotolerant and barophilic growth. Adv Aquat Microbiol 2:49–76

    CAS  Google Scholar 

  21. 21.

    Chilukuri LN, Fortes PG, Bartlett DH (1997) High pressure modulation of Escherichia coli DNA gyrase activity. Biochem Bioph Res Co 239:552–556

    CAS  Article  Google Scholar 

  22. 22.

    Larkin J, Stokes J (1966) Isolation of psychrophilic species of Bacillus. J Bacteriol 91:1667–1671

    CAS  Article  Google Scholar 

  23. 23.

    Dick J, De Windt W, De Graef B, Saveyn H, Van der Meeren P, De Belie N, Verstraete W (2006) Bio-deposition of a calcium carbonate layer on degraded limestone by Bacillus species. Biodegradation 17:357–367

    CAS  Article  Google Scholar 

  24. 24.

    Larkin JM, Stokes JL (1967) Taxonomy of psychrophilic strains of Bacillus. J Bacteriol 94:889–895. https://doi.org/10.1128/jb.94.4.889-895.1967

    CAS  Article  PubMed  PubMed Central  Google Scholar 

  25. 25.

    Micallef R, Vella D, Sinagra E, Zammit G (2016) Biocalcifying Bacillus subtilis cells effectively consolidate deteriorated Globigerina limestone. J Ind Microbiol Biotechnol 43:941–952. https://doi.org/10.1007/s10295-016-1768-0

    CAS  Article  PubMed  Google Scholar 

  26. 26.

    Yayanos AA, Boxtel RV (1982) Coupling device for quick high-pressure connections to 100 MPa. Rev Sci Instrum 53:704–705. https://doi.org/10.1063/1.1137011

    Article  Google Scholar 

  27. 27.

    Li S, Xiao X, Li J, Luo J, Wang F (2006) Identification of genes regulated by changing salinity in the deep-sea bacterium Shewanella sp. WP3 using RNA arbitrarily primed PCR. Extremophiles 10:97–104. https://doi.org/10.1007/s00792-005-0476-x

    CAS  Article  PubMed  Google Scholar 

  28. 28.

    Larkin MA, Blackshields G, Brown N, Chenna R, McGettigan PA, McWilliam H, Valentin F, Wallace IM, Wilm A, Lopez R (2007) Clustal W and Clustal X version 2.0. Bioinformatics 23:2947–2948. https://doi.org/10.1093/bioinformatics/btm404

    CAS  Article  PubMed  Google Scholar 

  29. 29.

    Saitou N, Nei M (1987) The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol 4:406–425. https://doi.org/10.1093/oxfordjournals.molbev.a040454

    CAS  Article  Google Scholar 

  30. 30.

    Tamura K, Stecher G, Peterson D, Filipski A, Kumar S (2013) MEGA6: molecular evolutionary genetics analysis version 6.0. Mol Biol Evol 30:2725–2729. https://doi.org/10.1093/molbev/mst197

    CAS  Article  PubMed  PubMed Central  Google Scholar 

  31. 31.

    Andrews S (2010) FastQC: a quality control tool for high throughput sequence data

  32. 32.

    Bolger AM, Lohse M, Usadel B (2014) Trimmomatic: a flexible trimmer for Illumina sequence data. Bioinformatics 30:2114–2120. https://doi.org/10.1093/bioinformatics/btu170

    CAS  Article  PubMed  PubMed Central  Google Scholar 

  33. 33.

    Langmead B, Salzberg SL (2012) Fast gapped-read alignment with bowtie 2. Nat Methods 9:357–359

    CAS  Article  Google Scholar 

  34. 34.

    Wagner GP (2012) Measurement of mRNA abundance using RNA-seq data RPKM measure is inconsistent among samples. Theory Biosci 131:281–285. https://doi.org/10.1007/s12064-012-0162-3

    CAS  Article  PubMed  Google Scholar 

  35. 35.

    Alexa A, Rahnenfuhrer J (2016) topGO: enrichment analysis for gene ontology. R package version 2.30.1

  36. 36.

    Ashburner M, Ball CA, Blake JA, Botstein D, Butler H, Cherry JM, Davis AP, Dolinski K, Dwight SS, Eppig JT, Harris MA, Hill DP, Issel-Tarver L, Kasarskis A, Lewis S, Matese JC, Richardson JE, Ringwald M, Rubin GM, Sherlock G (2000) Gene ontology: tool for the unification of biology. Nat Genet 25:25–29. https://doi.org/10.1038/75556

    CAS  Article  PubMed  PubMed Central  Google Scholar 

  37. 37.

    Bagg A, Neilands JB (1985) Mapping of a mutation affecting regulation of iron uptake systems in Escherichia coli K-12. J Bacteriol 161:450–453. https://doi.org/10.3182/20120829-3-MX-2028.00122

    CAS  Article  PubMed  PubMed Central  Google Scholar 

  38. 38.

    Que Q, Helmann JD (2000) Manganese homeostasis in Bacillus subtilis is regulated by MntR, a bifunctional regulator related to the diphtheria toxin repressor family of proteins. Mol Microbiol 35:1454–1468

    CAS  Article  Google Scholar 

  39. 39.

    Kaneda T (1991) Iso-and anteiso-fatty acids in bacteria: biosynthesis, function, and taxonomic significance. Microbiol Mol Biol R 55:288–302. https://doi.org/10.1128/mmbr.55.2.288-302.1991

    CAS  Article  Google Scholar 

  40. 40.

    ZoBell CE, Johnson FH (1949) The influence of hydrostatic pressure on the growth and viability of terrestrial and marine bacteria. J Bacteriol 57:179–189. https://doi.org/10.1128/jb.57.2.179-189.1949

    CAS  Article  PubMed  PubMed Central  Google Scholar 

  41. 41.

    Yayanos AA (1995) Microbiology to 10,500 meters in the deep sea. Annu Rev Microbiol 49:777–805. https://doi.org/10.1146/annurev.mi.49.100195.004021

    CAS  Article  PubMed  Google Scholar 

  42. 42.

    Yayanos AA, Dietz AS, Van Boxtel R (1982) Dependence of reproduction rate on pressure as a hallmark of deep-sea bacteria. Appl Environ Microbiol 44:1356–1361. https://doi.org/10.1128/aem.44.6.1356-1361.1982

    CAS  Article  PubMed  PubMed Central  Google Scholar 

  43. 43.

    Groisman EA, Hollands K, Kriner MA, Lee E-J, Park S-Y, Pontes MH (2013) Bacterial Mg2+ homeostasis, transport, and virulence. Annu Rev Genet 47:625–646. https://doi.org/10.1146/annurev-genet-051313-051025

    CAS  Article  PubMed  PubMed Central  Google Scholar 

  44. 44.

    Escolar L, Pérez-Martín J, De Lorenzo V (1999) Opening the iron box: transcriptional metalloregulation by the Fur protein. J Bacteriol 181:6223–6229. https://doi.org/10.1128/jb.181.20.6223-6229.1999

    CAS  Article  PubMed  PubMed Central  Google Scholar 

  45. 45.

    Hantke K (2001) Iron and metal regulation in bacteria. Curr Opin Microbiol 4:172–177. https://doi.org/10.1016/s1369-5274(00)00184-3

    CAS  Article  PubMed  Google Scholar 

  46. 46.

    Touati D (2000) Iron and oxidative stress in bacteria. Arch Biochem Biophys 373:1–6. https://doi.org/10.1006/abbi.1999.1518

    CAS  Article  PubMed  Google Scholar 

  47. 47.

    Hoffmann T, Schütz A, Brosius M, Völker A, Völker U, Bremer E (2002) High-salinity-induced iron limitation in Bacillus subtilis. J Bacteriol 184:718–727. https://doi.org/10.1128/jb.184.3.718-727.2002

    CAS  Article  PubMed  PubMed Central  Google Scholar 

  48. 48.

    Steil L, Hoffmann T, Budde I, Völker U, Bremer E (2003) Genome-wide transcriptional profiling analysis of adaptation of Bacillus subtilis to high salinity. J Bacteriol 185:6358–6370. https://doi.org/10.1128/jb.185.21.6358-6370.2003

    CAS  Article  PubMed  PubMed Central  Google Scholar 

  49. 49.

    Anjem A, Varghese S, Imlay JA (2009) Manganese import is a key element of the OxyR response to hydrogen peroxide in Escherichia coli. Mol Microbiol 72:844–858. https://doi.org/10.1111/j.1365-2958.2009.06699.x

    CAS  Article  PubMed  PubMed Central  Google Scholar 

  50. 50.

    Crosa JH, Walsh CT (2002) Genetics and assembly line enzymology of siderophore biosynthesis in Bacteria. Microbiol Mol Biol R 66:223–249. https://doi.org/10.1128/mmbr.66.2.223-249.2002

    CAS  Article  Google Scholar 

  51. 51.

    Schwartz CJ, Djaman O, Imlay JA, Kiley PJ (2000) The cysteine desulfurase, IscS, has a major role in in vivo Fe-S cluster formation in Escherichia coli. P Natl Acad Sci USA 97:9009–9014. https://doi.org/10.1073/pnas.160261497

    CAS  Article  Google Scholar 

  52. 52.

    Matsumura P, Marquis RE (1977) Energetics of streptococcal growth inhibition by hydrostatic pressure. Appl Environ Microbiol 33:885–892. https://doi.org/10.1128/aem.33.4.885-892.1977

    CAS  Article  PubMed  PubMed Central  Google Scholar 

  53. 53.

    Yancey PH (2005) Organic osmolytes as compatible, metabolic and counteracting cytoprotectants in high osmolarity and other stresses. J Exp Biol 208:2819–2830

    CAS  Article  Google Scholar 

  54. 54.

    Kempf B, Bremer E (1998) Uptake and synthesis of compatible solutes as microbial stress responses to high-osmolality environments. Arch Microbiol 170:319–330. https://doi.org/10.1007/s002030050649

    CAS  Article  PubMed  Google Scholar 

  55. 55.

    Martin D, Bartlett DH, Roberts MF (2002) Solute accumulation in the deep-sea bacterium Photobacterium profundum. Extremophiles 6:507–514

    CAS  Article  Google Scholar 

  56. 56.

    Amrani A, Bergon A, Holota H, Tamburini C, Garel M, Ollivier B, Imbert J, Dolla A, Pradel N (2014) Transcriptomics reveal several gene expression patterns in the piezophile Desulfovibrio hydrothermalis in response to hydrostatic pressure. PLoS One 9:e106831-e106831. https://doi.org/10.1371/journal.pone.0106831

    CAS  Article  Google Scholar 

  57. 57.

    Amrani A, van Helden J, Bergon A, Aouane A, Ben Hania W, Tamburini C, Loriod B, Imbert J, Ollivier B, Pradel N, Dolla A (2016) Deciphering the adaptation strategies of Desulfovibrio piezophilus to hydrostatic pressure through metabolic and transcriptional analyses. Environ Microbiol Rep 8:520–526. https://doi.org/10.1111/1758-2229.12427

    CAS  Article  PubMed  Google Scholar 

  58. 58.

    Kuhlmann AU, Bremer E (2002) Osmotically regulated synthesis of the compatible solute ectoine in Bacillus pasteurii and related Bacillus spp. Appl Environ Microbiol 68:772–783. https://doi.org/10.1128/aem.68.2.772-783.2002

    CAS  Article  PubMed  PubMed Central  Google Scholar 

  59. 59.

    Brands S, Schein P, Castro-Ochoa KF, Galinski EA (2019) Hydroxyl radical scavenging of the compatible solute ectoine generates two N-acetimides. Arch Biochem Biophys 674:108097. https://doi.org/10.1016/j.abb.2019.108097

    CAS  Article  PubMed  Google Scholar 

  60. 60.

    Singh BK, Shaner DL (1995) Biosynthesis of branched chain amino acids: from test tube to field. Plant Cell 7:935–944. https://doi.org/10.1105/tpc.7.7.935

    CAS  Article  PubMed  PubMed Central  Google Scholar 

  61. 61.

    De Mendoza D, Ulrich AK, Cronan JE (1983) Thermal regulation of membrane fluidity in Escherichia coli. Effects of overproduction of beta-ketoacyl-acyl carrier protein synthase I. J Biol Chem 258:2098–2101

    Article  Google Scholar 

  62. 62.

    Allen EE, Facciotti D, Bartlett DH (1999) Monounsaturated but not polyunsaturated fatty acids are required for growth of the deep-sea bacterium Photobacterium profundum SS9 at high pressure and low temperature. Appl Environ Microbiol 65:1710–1720. https://doi.org/10.1128/aem.65.4.1710-1720.1999

    CAS  Article  PubMed  PubMed Central  Google Scholar 

  63. 63.

    Allen EE, Bartlett DH (2000) FabF is required for piezoregulation of cis-vaccenic acid levels and piezophilic growth of the deep-sea bacterium Photobacterium profundum strain SS9. J Bacteriol 182:1264–1271

    CAS  Article  Google Scholar 

  64. 64.

    Wang F, Xiao X, Ou H-Y, Gai Y, Wang F (2009) The role and regulation of fatty acid biosynthesis in Shewanella piezotolerans WP3 response to different temperatures and pressures. J Bacteriol 191:2574–2584. https://doi.org/10.1128/jb.00498-08

    CAS  Article  PubMed  PubMed Central  Google Scholar 

  65. 65.

    Oger PM, Jebbar M (2010) The many ways of coping with pressure. Res Microbiol 161:799–809. https://doi.org/10.1016/j.resmic.2010.09.017

    Article  PubMed  Google Scholar 

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Funding

This study was financially supported by the National Key Research and Development Program of China (No. 2018YFC0309800) and the National Natural Science Foundation of China (grant nos. 41776173, 41530967, 91951117, and 41921006).

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HW, YZ, and XX were involved in experimental design. HW conducted the experimental procedure and analyzed the data. HW, YZ, and XX wrote the manuscript. DB made comments and suggestions to improve the manuscript. All authors read and approved the manuscript.

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Correspondence to Yu Zhang.

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The authors declare that they have no conflict of interest.

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This article does not contain any studies with human participants or animals performed by any of the authors.

Data Accessibility

All sequence reads have been deposited in the NCBI Sequence Read Archive (SRA) database (https://www.ncbi.nlm.nih.gov/sra) and are accessible through Bioproject accession number PRJNA577046.

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Wang, H., Zhang, Y., Bartlett, D.H. et al. Transcriptomic Analysis Reveals Common Adaptation Mechanisms Under Different Stresses for Moderately Piezophilic Bacteria. Microb Ecol 81, 617–629 (2021). https://doi.org/10.1007/s00248-020-01609-3

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Keywords

  • Common adaptation
  • Transcriptome
  • MgCl2
  • Piezophile
  • High pressure
  • Stress