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Review
Denitrifying Woodchip Bioreactors: A Microbial Solution for Nitrate in Agricultural Wastewater—A Review
Sua Lee , Min Cho , Michael J. Sadowsky , Jeonghwan Jang
J. Microbiol. 2023;61(9):791-805.   Published online August 18, 2023
DOI: https://doi.org/10.1007/s12275-023-00067-z
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AbstractAbstract
Nitrate ( NO3 −) is highly water-soluble and considered to be the main nitrogen pollutants leached from agricultural soils. Its presence in aquatic ecosystems is reported to cause various environmental and public health problems. Bioreactors containing microbes capable of transforming NO3 − have been proposed as a means to remediate contaminated waters. Woodchip bioreactors (WBRs) are continuous flow, reactor systems located below or above ground. Below ground systems are comprised of a trench filled with woodchips, or other support matrices. The nitrate present in agricultural drainage wastewater passing through the bioreactor is converted to harmless dinitrogen gas ( N2) via the action of several bacteria species. The WBR has been suggested as one of the most cost-effective NO3 −-removing strategy among several edge-of-field practices, and has been shown to successfully remove NO3 − in several field studies. NO3 − removal in the WBR primarily occurs via the activity of denitrifying microorganisms via enzymatic reactions sequentially reducing NO3 − to N2. While previous woodchip bioreactor studies have focused extensively on its engineering and hydrological aspects, relatively fewer studies have dealt with the microorganisms playing key roles in the technology. This review discusses NO3 − pollution cases originating from intensive farming practices and N-cycling microbial metabolisms which is one biological solution to remove NO3 − from agricultural wastewater. Moreover, here we review the current knowledge on the physicochemical and operational factors affecting microbial metabolisms resulting in removal of NO3 − in WBR, and perspectives to enhance WBR performance in the future.

Citations

Citations to this article as recorded by  
  • Complete genome sequence of Neobacillus sp. strain OS1-2, a denitrifying bacterium isolated from apple orchard soil
    Jinwoo Ahn, Jeonghwan Jang, Elinne Becket
    Microbiology Resource Announcements.2025;[Epub]     CrossRef
  • Dissimilatory nitrate reductions in soil Neobacillus and Bacillus strains under aerobic condition
    Seohyun Ahn, Min Cho, Michael J. Sadowsky, Jeonghwan Jang
    Journal of Microbiology.2025; 63(2): e2411019.     CrossRef
  • Mn-oxidizing microalgae and woodchip-denitrifying bioreactor system for recovering manganese and removing nitrogen from electrolytic manganese metal industrial tailwater
    Xinyue Gong, Qin Peng, Ruixin Jiang, Na Yang, Cijun Xing, Rui Wang
    Journal of Hazardous Materials.2025; 488: 137383.     CrossRef
Journal Articles
Comparative analysis of the colistin resistance-regulating gene cluster in Klebsiella species
Sun Ju Kim , Hongbaek Cho , Kwan Soo Ko
J. Microbiol. 2022;60(5):461-468.   Published online April 18, 2022
DOI: https://doi.org/10.1007/s12275-022-1640-z
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AbstractAbstract
CrrAB two-component regulatory system is associated with colistin resistance in Klebsiella pneumoniae. Recently, some K. pneumoniae isolates lacking crrAB genes have been identified. In this study, we investigated the distribution and structural variation of the crrBAC-kexD cluster. To evaluate the structural variation of the crrBAC-kexD cluster, we explored 59 clinical K. pneumoniae isolates from Korea, and 508 whole genomes of K. pneumoniae and other strains of Klebsiella sp. Significant structural variations in crrBAC-kexD and its surrounding regions were identified among K. pneumoniae genomes. Within the genus Klebsiella, the cluster was identified only in K. pneumoniae, K. variicola, and K. quasipneumoniae, which form the K. pneumoniae complex. Among the 304 available K. pneumoniae genomes, an intact crrBAC-kexD cluster was identified in 178 isolates (58.6%), while the cluster was absent in 90 isolates (29.6%). Partial deletions within the cluster were identified in 22 genomes (7.2%). The most diverse structural patterns of the crrBAC-kexD cluster were observed in ST11 strains. Some clades lacked the crrBAC-kexD cluster. The crrBAC-kexD cluster was identified in the genomes of other bacterial species, including Citrobacter freundii and Enterobacter ludwigii. The crrBAC-kexD cluster is proposed to have been acquired by the ancestor of the K. pneumoniae complex from other bacterial species and the cluster may have been lost and re-acquired repeatedly in K. pneumoniae strains according to the phylogenetic analysis. The dynamic evolution of the crrBAC-kexD cluster suggests that it may have other roles, in addition to colistin resistance, in bacterial physiology.

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  • Roles of crrAB two-component regulatory system in Klebsiella pneumoniae: growth yield, survival in initial colistin treatment stage, and virulence
    Sun Ju Kim, Jong Hyun Shin, Hyunkeun Kim, Kwan Soo Ko
    International Journal of Antimicrobial Agents.2024; 63(1): 107011.     CrossRef
  • High prevalence of polymyxin-heteroresistant carbapenem-resistant Klebsiella pneumoniae and its within-host evolution to resistance among critically ill scenarios
    Xiaoli Wang, Tianjiao Meng, Yunqi Dai, Hong-Yu Ou, Meng Wang, Bin Tang, Jingyong Sun, Decui Cheng, Tingting Pan, Ruoming Tan, Hongping Qu
    Infection.2024;[Epub]     CrossRef
  • Role of efflux pumps, their inhibitors, and regulators in colistin resistance
    Yinhuan Ding, Jingchen Hao, Weijia Xiao, Caihong Ye, Xue Xiao, Chunxia Jian, Min Tang, Guangrong Li, Jinbo Liu, Zhangrui Zeng
    Frontiers in Microbiology.2023;[Epub]     CrossRef
Paraburkholderia lacunae sp. nov., isolated from soil near an artificial pond
Tingye Feng , Sang Eun Jeong , Jin Ju Lim , Seogang Hyun , Che Ok Jeon
J. Microbiol. 2019;57(4):232-237.   Published online January 16, 2019
DOI: https://doi.org/10.1007/s12275-019-8463-6
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AbstractAbstract
A Gram-stain-negative, strictly aerobic bacterial strain, designated strain S27T, was isolated from soil near an artificial pond in South Korea. Cells were non-motile short rods showing oxidase- and catalase-positive activities. Growth of strain S27T was observed at 20–40°C (optimum, 30°C), pH 5.0–7.0 (optimum, pH 6.0), and 0–0.5% (w/v) NaCl (optimum, 0%). Ubiquinone-8 was detected as the sole respiratory quinone and the major fatty acids were C16:0, cyclo-C17:0, and cyclo- C19:0 ω8c. The G + C content of the genomic DNA was 62.4 mol%. Phosphatidylglycerol, phosphatidylethanolamine, and an unidentified aminophospholipid were detected as the major polar lipids. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain S27T formed a clearly distinct phyletic lineage from closely related Paraburkholderia species within the genus Paraburkholderia. Strain S27T was most closely related to Paraburkholderia rhynchosiae WSM3937T, Paraburkholderia ginsengiterrae DCY85T, Paraburkholderia fungorum NBRC 102489T, and Paraburkholderia graminis C4D1MT with 98.8%, 98.4%, 98.4%, and 97.7% 16S rRNA gene sequence similarities, respectively. The DNA-DNA relatedness level between strain S27T and the type strain of P. rhynchosiae was 36.8 ± 2.6%. On the basis of phenotypic, chemotaxonomic and molecular properties, strain S27T represents a novel species of the genus Paraburkholderia, for which the name Paraburkholderia lacunae sp. nov. is proposed. The type strain is S27T (KACC 19714 T = JCM 32721T).

Citations

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  • International Committee on Systematics of Prokaryotes, Subcommittee on the taxonomy of Rhizobia and Agrobacteria, minutes of the annual meeting by videoconference, 5 July 2021, followed by online discussion until 31 December 2021
    Seyed Abdollah Mousavi, J. Peter W. Young
    International Journal of Systematic and Evolutionary Microbiology.2022;[Epub]     CrossRef
  • Lysobacter arenosi sp. nov. and Lysobacter solisilvae sp. nov. isolated from soil
    Kyeong Ryeol Kim, Kyung Hyun Kim, Shehzad Abid Khan, Hyung Min Kim, Dong Min Han, Che Ok Jeon
    Journal of Microbiology.2021; 59(8): 709.     CrossRef
  • The history and distribution of nodulating Paraburkholderia, a potential inoculum for Fynbos forage species
    Chrizelle W. Beukes, Stephanus N. Venter, Emma T. Steenkamp
    Grass and Forage Science.2021; 76(1): 10.     CrossRef
  • International Committee on Systematics of Prokaryotes Subcommittee on the Taxonomy of Rhizobia and Agrobacteria Minutes of the closed meeting by videoconference, 17 July 2019
    Philippe de Lajudie, J. Peter W. Young
    International Journal of Systematic and Evolutionary Microbiology .2020; 70(5): 3563.     CrossRef
  • Flavihumibacter soli sp. nov., Isolated from Soil
    Ye Lin Seo, Jaejoon Jung, Shehzad Abid Khan, Kyung Hyun Kim, Che Ok Jeon
    Current Microbiology.2020; 77(10): 3179.     CrossRef
  • List of new names and new combinations that have appeared in effective publications outside of the IJSEM and are submitted for valid publication
    Aharon Oren, George M. Garrity
    International Journal of Systematic and Evolutionary Microbiology .2019;[Epub]     CrossRef

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