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

  • Dockyu Kim
  • Ha Ju Park
  • Woo Jun Sul
  • Hyun Park
Original Article


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.


Biodegradation Degradation pathway Humic substances Low temperature Soil bacteria 


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)


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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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