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Folia Microbiologica

, Volume 63, Issue 3, pp 315–323 | Cite as

Transcriptome analysis of Pseudomonas sp. from subarctic tundra soil: pathway description and gene discovery for humic acids degradation

Original Article

Abstract

Although humic acids (HA) are involved in many biological processes in soils and thus their ecological importance has received much attention, the degradative pathways and corresponding catalytic genes underlying the HA degradation by bacteria remain unclear. To unveil those uncertainties, we analyzed transcriptomes extracted from Pseudomonas sp. PAMC 26793 cells time-dependently induced in the presence of HA in a lab flask. Out of 6288 genes, 299 (microarray) and 585 (RNA-seq) were up-regulated by > 2.0-fold in HA-induced cells, compared with controls. A significant portion (9.7% in microarray and 24.1% in RNA-seq) of these genes are predicted to function in the transport and metabolism of small molecule compounds, which could result from microbial HA degradation. To further identify lignin (a surrogate for HA)-degradative genes, 6288 protein sequences were analyzed against carbohydrate-active enzyme database and a self-curated list of putative lignin degradative genes. Out of 19 genes predicted to function in lignin degradation, several genes encoding laccase, dye-decolorizing peroxidase, vanillate O-demethylase oxygenase and reductase, and biphenyl 2,3-dioxygenase were up-regulated > 2.0-fold in RNA-seq. This induction was further confirmed by qRT-PCR, validating the likely involvement of these genes in the degradation of HA.

Keywords

Biodegradation Degradation pathway Humic substances Low temperature Soil bacteria 

Notes

Funding information

This work was supported by the grants, Functional genomic studies on microbial degradation/conversion pathways of polar soil humic substances (PE13300), The Antarctic organisms: cold-adaptation mechanisms and its application (PE16070), and Modeling responses of terrestrial organisms to environmental changes on King George Island (PE17090), funded by the Korea Polar Research Institute.

Supplementary material

12223_2017_573_MOESM1_ESM.xls (2.1 mb)
Supplementary Table S1 (XLS 2150 kb)
12223_2017_573_MOESM2_ESM.xlsx (259 kb)
Supplementary Table S2 (XLSX 259 kb)

References

  1. Ahmad M, Roberts JN, Hardiman EM, Singh R, Eltis LD, Bugg TD (2011) Identification of DypB from Rhodococcusjostii RHA1 as a lignin peroxidase. Biochemistry 50(23):5096–5107.  https://doi.org/10.1021/bi101892z CrossRefPubMedGoogle Scholar
  2. Anders S, Huber W (2010) Differential expression analysis for sequence count data. Genome Biol 11(10):R106.  https://doi.org/10.1186/gb-2010-11-10-r106 CrossRefPubMedPubMedCentralGoogle Scholar
  3. Bugg TD, Ahmad M, Hardiman EM, Rahmanpour R (2011a) Pathways for degradation of lignin in bacteria and fungi. Nat Prod Rep 28(12):1883–1896.  https://doi.org/10.1039/c1np00042j CrossRefPubMedGoogle Scholar
  4. Bugg TD, Ahmad M, Hardiman EM, Singh R (2011b) The emerging role for bacteria in lignin degradation and bio-product formation. Curr Opin Biotechnol 22:394–400CrossRefPubMedGoogle Scholar
  5. Cantarel BL, Coutinho PM, Rancurel C, Bernard T, Lombard V, Henrissat B (2009) The Carbohydrate-Active EnZymes database (CAZy): an expert resource for Glycogenomics. Nucleic Acids Res 37(Database issue):D233–D238CrossRefPubMedGoogle Scholar
  6. Cruz A, Rodrigues R, Pinheiro M, Mendo S (2015) Transcriptomes analysis of Aeromonasmolluscorum Av27 cells exposed to tributyltin (TBT): unravelling the effects from the molecular level to the organism. Mar Environ Res 109:132–139CrossRefPubMedPubMedCentralGoogle Scholar
  7. Dari K, Béchet M, Blondeau R (1995) Isolation of soil Streptomyces strains capable of degrading humic acids and analysis of their peroxidase activity. FEMS Microbiol Ecol 16(2):115–122.  https://doi.org/10.1111/j.1574-6941.1995.tb00275.x CrossRefGoogle Scholar
  8. Esham EC, Ye W, Moran MA (2000) Identification and characterization of humic substances-degrading bacterial isolates from an estuarine environment. FEMS Microbiol Ecol 34(2):103–111.  https://doi.org/10.1111/j.1574-6941.2000.tb00759.x CrossRefPubMedGoogle Scholar
  9. Freedman Z, Zak DR (2014) Atmospheric N deposition increases bacterial laccase-like multicopper oxidases: implications for organic matter decay. Appl Environ Microbiol 80(14):4460–4468.  https://doi.org/10.1128/AEM.01224-14 CrossRefPubMedPubMedCentralGoogle Scholar
  10. Gramss G, Ziegenhagen D, Sorge S (1999) Degradation of soil humic extract by wood- and soil-associated fungi, bacteria, and commercial enzymes. Microb Ecol 37:140–151CrossRefPubMedGoogle Scholar
  11. Grinhut T, Hadar Y, Chen Y (2007) Degradation and transformation of humic substances by saprotrophic fungi: processes and mechanisms. Fungal Biol Rev 21(4):179–189.  https://doi.org/10.1016/j.fbr.2007.09.003 CrossRefGoogle Scholar
  12. Grinhut T, Hertkorn N, Schmitt-Kopplin P, Hadar Y, Chen Y (2011) Mechanisms of humic acids degradation by white rot fungi explored using 1H NMR spectroscopy and FTICR mass spectrometry. Environ Sci Technol 45(7):2748–2754.  https://doi.org/10.1021/es1036139 CrossRefPubMedGoogle Scholar
  13. Im JH, Kim MG, Kim ES (2007) Comparative transcriptome analysis for avermectin overproduction via Streptomyces avermitilis microarray system. J Microbiol Biotechnol 17:534–538PubMedGoogle Scholar
  14. Kim D, Kim YS, Kim SK, Kim SW, Zylstra GJ, Kim YM, Kim E (2002) Monocyclic aromatic hydrocarbon degradation by Rhodococcus sp. strain DK17. Appl Environ Microbiol 68:3270–3278CrossRefPubMedPubMedCentralGoogle Scholar
  15. Kim D, Chae JC, Zylstra GJ, Kim YS, Kim SK, Nam MH, Kim YM, Kim E (2004) Identification of a novel dioxygenase involved in metabolism of o-xylene, toluene, and ethylbenzene by Rhodococcus sp. strain DK17. Appl Environ Microbiol 70:7086–7092CrossRefPubMedPubMedCentralGoogle Scholar
  16. Lee SH, Jang I, Chae N, Choi T, Kang H (2013) Organic layer serves as a hotspot of microbial activity and abundance in Arctic tundra soils. Microb Ecol 65:405–414CrossRefPubMedGoogle Scholar
  17. Lin L, Cheng Y, Pu Y, Sun S, Li X, Jin M, Pierson EA, Gross DC, Dale BE, Dai SY, Ragauskas AJ, Yuan JS (2016) Systems biology-guided biodesign of consolidated lignin conversion. Green Chem 18:5536–5547.  https://doi.org/10.1039/C6GC01131D
  18. Masai E, Katayama Y, Fukuda M (2007) Genetic and biochemical investigations on bacterial catabolic pathways for lignin-derived aromatic compounds. Biosci Biotechnol Biochem 71:1–15CrossRefPubMedGoogle Scholar
  19. Newsham KK, Hopkins DW, Carvalhais LC, Fretwell PT, Rushton SP, O’Donnell AG, Dennis PG (2016) Relationship between soil fungal diversity and temperature in the maritime Antarctic. Nat Clim Chang 6:182–186CrossRefGoogle Scholar
  20. Park HJ, Kim D (2015) Isolation and characterization of humic substances-degrading bacteria from the subarctic Alaska grasslands. J Basic Microbiol 55(1):54–61.  https://doi.org/10.1002/jobm.201300087 CrossRefPubMedGoogle Scholar
  21. Park BH, Karpinets TV, Syed MH, Leuze MR, Uberbacher EC (2010) CAZymes Analysis Toolkit (CAT): web service for searching and analyzing carbohydrate-active enzymes in a newly sequenced organism using CAZy database. Glycobiology 20(12):1574–1584.  https://doi.org/10.1093/glycob/cwq106 CrossRefPubMedGoogle Scholar
  22. Park HJ, Chae N, Sul WJ, Lee BY, Lee YK, Kim D (2015) Temporal changes in soil bacterial diversity and humic substances degradation in subarctic tundra soil. Microb Ecol 69:668–675CrossRefPubMedGoogle Scholar
  23. Pollegioni L, Tonin F, Rosini E (2015) Lignin-degrading enzymes. FEBS J 282:1190–1213CrossRefPubMedGoogle Scholar
  24. Sainsbury PD, Hardiman EM, Ahmad M, Otani H, Seghezzi N, Eltis LD, Bugg TD (2013) Breaking down lignin to high-value chemicals: the conversion of lignocellulose to vanillin in a gene deletion mutant of Rhodococcusjostii RHA1. ACS Chem Biol 8(10):2151–2156.  https://doi.org/10.1021/cb400505a CrossRefPubMedGoogle Scholar
  25. Stevenson FJ (1994) Humus chemistry: genesis, composition, reactions, 2nd edn. John Wiley & Sons, New YorkGoogle Scholar
  26. Sul WJ, Park J, Quensen JF 3rd, Rodrigues JL, Seliger L, Tsoi TV, Zylstra GJ, Tiedje JM (2009) DNA-stable isotope probing integrated with metagenomics for retrieval of biphenyl dioxygenase genes from polychlorinated biphenyl-contaminated river sediment. Appl Environ Microbiol 75(17):5501–5506.  https://doi.org/10.1128/AEM.00121-09 CrossRefPubMedPubMedCentralGoogle Scholar
  27. Van Trump JI, Sun Y, Coates JD (2006) Microbial interactions with humic substances. Adv Appl Microbiol 60:55–96CrossRefPubMedGoogle Scholar
  28. Wang Y, Gao S, Li C, Zhang J, Wang L (2016) Effects of temperature on soil organic carbon fractions contents, aggregate stability and structural characteristics of humic substances in a Mollisol. J Soils Sediments 16(7):1849–1857.  https://doi.org/10.1007/s11368-016-1379-4 CrossRefGoogle Scholar
  29. Yang JW, Zheng DJ, Cui BD, Yang M, Chen YZ (2016) RNA-seq transcriptome analysis of a Pseudomonas strain with diversified catalytic properties growth under different culture medium. Microbiology 5:626–636Google Scholar

Copyright information

© Institute of Microbiology, Academy of Sciences of the Czech Republic, v.v.i. 2017

Authors and Affiliations

  1. 1.Division of Life SciencesKorea Polar Research InstituteIncheonSouth Korea
  2. 2.Department of Systems BiotechnologyChung-Ang UniversityAnseongSouth Korea

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