- Ammonia-oxidizing archaea in biological interactions
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Jong-Geol Kim , Khaled S. Gazi , Samuel Imisi Awala , Man-Young Jung , Sung-Keun Rhee
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J. Microbiol. 2021;59(3):298-310. Published online February 23, 2021
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DOI: https://doi.org/10.1007/s12275-021-1005-z
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 Abstract
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The third domain Archaea was known to thrive in extreme or
anoxic environments based on cultivation studies. Recent metagenomics-
based approaches revealed a widespread abundance
of archaea, including ammonia-oxidizing archaea (AOA)
of Thaumarchaeota in non-extreme and oxic environments.
AOA alter nitrogen species availability by mediating the first
step of chemolithoautotrophic nitrification, ammonia oxidation
to nitrite, and are important primary producers in ecosystems,
which affects the distribution and activity of other
organisms in ecosystems. Thus, information on the interactions
of AOA with other cohabiting organisms is a crucial
element in understanding nitrogen and carbon cycles in ecosystems
as well as the functioning of whole ecosystems. AOA
are self-nourishing, and thus interactions of AOA with other
organisms can often be indirect and broad. Besides, there are
possibilities of specific and obligate interactions. Mechanisms
of interaction are often not clearly identified but only inferred
due to limited knowledge on the interaction factors analyzed
by current technologies. Here, we overviewed different types
of AOA interactions with other cohabiting organisms, which
contribute to understanding AOA functions in ecosystems.
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Citations
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Heather Schiller, Yirui Hong, Joshua Kouassi, Theopi Rados, Jasmin Kwak, Anthony DiLucido, Daniel Safer, Anita Marchfelder, Friedhelm Pfeiffer, Alexandre Bisson, Stefan Schulze, Mechthild Pohlschroder
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Zhao Chen, Jian Li, Qianqian Zhai, Zhiqiang Chang, Jitao Li
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Journal of Microbiology.2021; 59(3): 229. CrossRef
- Comparative genomic analysis of Geosporobacter ferrireducens and its versatility of anaerobic energy metabolism
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Man-Young Jung , So-Jeong Kim , Jong-Geol Kim , Heeji Hong , Joo-Han Gwak , Soo-Je Park , Yang-Hoon Kim , Sung-Keun Rhee
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J. Microbiol. 2018;56(5):365-371. Published online May 2, 2018
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DOI: https://doi.org/10.1007/s12275-018-7451-6
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74
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Abstract
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Members of the family Clostridiaceae within phylum Firmicutes
are ubiquitous in various iron-reducing environments.
However, genomic data on iron-reducing bacteria of the family
Clostridiaceae, particularly regarding their environmental
distribution, are limited. Here, we report the analysis and
comparison of the genomic properties of Geosporobacter
ferrireducens IRF9, a strict anaerobe that ferments sugars
and degrades toluene under iron-reducing conditions, with
those of the closely related species, Geosporobacter subterraneus
DSM 17957. Putative alkyl succinate synthase-encoding
genes were observed in the genome of strain IRF9 instead
of the typical benzyl succinate synthase-encoding genes.
Canonical genes associated with iron reduction were not
observed in either genome. The genomes of strains IRF9 and
DMS 17957 harbored genes for acetogenesis, that encode two
types of Rnf complexes mediating the translocation of H+
and Na+ ions, respectively. Strain IRF9 harbored two different
types of ATPases (Na+-dependent F-type ATPase and H+-
dependent V-type ATPase), which enable full exploitation
of ion gradients. The versatile energy conservation potential
of strain IRF9 promotes its survival in various environmental
conditions.
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Citations
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World Journal of Microbiology and Biotechnology.2021;[Epub] CrossRef - Maize straw biochar addition inhibited pentachlorophenol dechlorination by strengthening the predominant soil reduction processes in flooded soil
Min Zhu, Xiaofei Lv, Ashley E. Franks, Philip C. Brookes, Jianming Xu, Yan He
Journal of Hazardous Materials.2020; 386: 122002. CrossRef - New Frontiers of Anaerobic Hydrocarbon Biodegradation in the Multi-Omics Era
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Frontiers in Microbiology.2019;[Epub] CrossRef
- A novel methanotroph in the genus Methylomonas that contains a distinct clade of soluble methane monooxygenase
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Ngoc-Loi Nguyen , Woon-Jong Yu , Hye-Young Yang , Jong-Geol Kim , Man-Young Jung , Soo-Je Park , Seong-Woon Roh , Sung-Keun Rhee
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J. Microbiol. 2017;55(10):775-782. Published online September 28, 2017
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DOI: https://doi.org/10.1007/s12275-017-7317-3
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70
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Abstract
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Aerobic methane oxidation is a key process in the global carbon
cycle that acts as a major sink of methane. In this study,
we describe a novel methanotroph designated EMGL16-1
that was isolated from a freshwater lake using the floating
filter culture technique. Based on a phylogenetic analysis of
16S rRNA gene sequences, the isolate was found to be closely
related to the genus Methylomonas in the family Methylococcaceae
of the class Gammaproteobacteria with 94.2–97.4%
16S rRNA gene similarity to Methylomonas type strains. Comparison
of chemotaxonomic and physiological properties
further suggested that strain EMGL16-1 was taxonomically
distinct from other species in the genus Methylomonas. The
isolate was versatile in utilizing nitrogen sources such as molecular
nitrogen, nitrate, nitrite, urea, and ammonium. The
genes coding for subunit of the particulate form methane
monooxygenase (pmoA), soluble methane monooxygenase
(mmoX), and methanol dehydrogenase (mxaF) were detected
in strain EMGL16-1. Phylogenetic analysis of mmoX indicated
that mmoX of strain EMGL16-1 is distinct from those
of other strains in the genus Methylomonas. This isolate probably
represents a novel species in the genus. Our study provides
new insights into the diversity of species in the genus
Methylomonas and their environmental adaptations.
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Citations
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Nature Communications.2023;[Epub] CrossRef -
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International Journal of Systematic and Evolutionary Microbiology
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International Journal of Systematic and Evolutionary Microbiology
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- Calculibacillus koreensis gen. nov., sp. nov., an anaerobic Fe(III)-reducing bacterium isolated from sediment of mine tailings
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Ui-Gi Min , So-Jeong Kim , Heeji Hong , Song-Gun Kim , Joo-Han Gwak , Man-Young Jung , Jong-Geol Kim , Jeong-Geol Na , Sung-Keun Rhee
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J. Microbiol. 2016;54(6):413-419. Published online May 27, 2016
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DOI: https://doi.org/10.1007/s12275-016-6086-8
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76
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Abstract
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A strictly anaerobic bacterium, strain B5T, was isolated from
sediment of an abandoned coal mine in Taebaek, Republic
of Korea. Cells of strain B5T were non-spore-forming, straight,
Gram-positive rods. The optimum pH and temperature for
growth were pH 7.0 and 30°C, respectively, while the strain
was able to grow within pH and temperature ranges of 5.5–
7.5 and 25–45°C, respectively. Growth of strain B5T was
observed at NaCl concentrations of 0 to 6.0% (w/v) with an
optimum at 3.0–4.0% (w/v). The polar lipids consisted of
phosphatidylethanolamine, phosphatidylglycerol, an unknown
phospholipid and three unknown polar lipids. Strain B5T
grew anaerobically by reducing nitrate, nitrite, ferric-citrate,
ferric-nitrilotriacetate, elemental sulfur, thiosulfate, and anthraquinone-
2-sulfonate in the presence of proteinaceous compounds,
organic acids, and carbohydrates as electron donors.
The isolate was not able to grow by fermentation. Strain B5T
did not grow under aerobic or microaerobic conditions. Phylogenetic
analysis based on 16S rRNA gene sequences showed
that strain B5T is most closely related to the genus Tepidibacillus
(T. fermentans STGHT; 96.3%) and Vulcanibacillus
(V. modesticaldus BRT; 94.6%). The genomic DNA G+C content
(36.9 mol%) of strain B5T was higher than those of T.
fermentans STGHT (34.8 mol%) and V. modesticaldus BRT
(34.5 mol%). Based on its phenotypic, chemotaxonomic, and
phylogenetic properties, we describe a new species of a novel
genus Calculibacillus, represented by strain B5T (=KCTC
15397T =JCM 19989T), for which we propose the name Calculibacillus
koreensis gen. nov., sp. nov.
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