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
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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
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
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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
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
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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
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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