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

2022-03-24T07:11:26Z

Title: Transcriptome analysis of Pseudomonas sp. from subarctic tundra soil: pathway description and gene discovery for humic acids degradation Authors: Kim, Dockyu; Park, Hyun; Sul, Woo Jun; Park, Ha Ju 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 6,288 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, 6,288 protein sequences were analyzed against CAZy 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.

Functional genomic studies on microbial degradation/conversion pathways of polar soil humic substances

2022-03-24T07:11:58Z

Title: Functional genomic studies on microbial degradation/conversion pathways of polar soil humic substances Authors: Kim, Dockyu

Isolation and characterization of humic substances-degrading bacteria from the subarctic Alaska grasslands

2022-03-24T07:13:58Z

Title: Isolation and characterization of humic substances-degrading bacteria from the subarctic Alaska grasslands Authors: Kim, Dockyu; Park, Ha Ju Abstract: Humic substances (HS), an important fraction of soil organic carbon, are distributed widely throughout cold environments. A total of cold-adapted 122 bacterial strains were isolated from 66 Alaska grassland soil samples based on their ability to grow on humic acids (HA), a main fraction of HS, as a carbon and energy source. These isolates were identified based on 16S rRNA gene sequencing, with class Bacilli (79.5%) and γ-Proteobacteria (17.1%) comprising the largest groups. Among them, forty-five strains, mainly Paenibacillus (27 strains) and Pseudomonas (15 strains), were selected for further screening. Two strains (Pseudomonas sp. PAMC 26793 and Paenibacillus sp. PAMC 26794) most efficiently degraded HA, but showed significant differences in their ability to grow on various monocyclic aromatics, which are putative degradative metabolites of HS. Fourier transform infrared spectra also showed substantial but different changes in HA chemical structure after incubation with each strain. Gel permeation chromatography demonstrated that depolymerization and polymerization of HA occurred during HS degradation by these newly isolated microbes.

Temporal changes in soil bacterial diversity and humic substances degradation in subarctic tundra soil

2022-03-24T07:12:52Z

Title: Temporal changes in soil bacterial diversity and humic substances degradation in subarctic tundra soil Authors: Park, Ha Ju; Kim, Dockyu; Lee, Yoo Kyung; Lee, Bang Yong; Sul, Woo Jun; Chae, Nam Yi Abstract: Humic substances (HS), primarily humic acids (HA) and fulvic acids (FA), are the largest constituent of soil organic matter. In microcosm systems with subarctic HS-rich tundra soil (site AK 1-75;approximately 5.6？C during the thawing period) from Council, Alaska, the HA content significantly decreased to 48% after 99 day-incubation at 5oC as part of a biologically-mediated process. Accordingly, levels of FA, a putative byproduct of HA degradation, consistently increased to 172% during an identical incubation process. Culture-independent microbial community analysis showed that during the microcosm experiments, the relative abundance of phyla Proteobacteria (bacteria) and Euryarchaeota (archaea) largely increased, indicating their involvement in HS degradation. When the indigenous bacteria in AK 1-75 were enriched in an artificial mineral medium spiked with HA, the changes in relative abundance were most conspicuous in Proteobacteria (from 60.2% to 79.0%), specifically Betaproteobacteria-related bacteria. One hundred twenty-two HA-degrading bacterial strains, primarily from the genera Paenibacillus (phylum Firmicutes) and Pseudomonas (class Gammaproteobacteria), were cultivated from AK 1-75 and nearby sites. Through culture-dependent analysis with these bacterial isolates, we observed increasing HS-degradation rates in parallel with rising temperatures in a range of 0 to 20？C, with the most notable increase occurring at 8？C compared to 6？C. Our results indicate that, although microbial-mediated HS degradation occurs at temperature as low as 5？C in tundra ecosystems, increasing soil temperature caused by global climate change could enhance HS degradation rates. Extending the thawing period could also increase degradation activity, thereby directly affecting nearby microbial communities and rhizosphere environments.