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Kim, Dae Suk,Kim, Dong Hyun,Lee, Hemin,Jee, Hyunjoong,Lee, Young,Chang, Min-youl,Kwak, Taek-jong,Kim, Chul-Hong,Shin, Young-Ah,Lee, Jeung-Hoon,Yoon, Tae-jin,Lee, Min-Geol S. Karger AG 2013 International archives of allergy and immunology Vol.162 No.2
<P>Abstract </P><P>No abstract available </P><P>Copyright © 2012 S. Karger AG, Basel</P>
Ammonia-oxidizing archaea in biological interactions
Kim Jong-Geol,Gazi Khaled S.,Awala Samuel Imisi,Jung Man-Young,이성근 한국미생물학회 2021 The journal of microbiology Vol.59 No.3
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.
Hydrogen peroxide detoxification is a key mechanism for growth of ammonia-oxidizing archaea
Kim, Jong-Geol,Park, Soo-Je,Sinninghe Damsté,, Jaap S.,Schouten, Stefan,Rijpstra, W. Irene C.,Jung, Man-Young,Kim, So-Jeong,Gwak, Joo-Han,Hong, Heeji,Si, Ok-Ja,Lee, SangHoon,Madsen, Eugene L.,Rh National Academy of Sciences 2016 PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF Vol.113 No.28
<P>Ammonia-oxidizing archaea (AOA), that is, members of the Thaumarchaeota phylum, occur ubiquitously in the environment and are of major significance for global nitrogen cycling. However, controls on cell growth and organic carbon assimilation by AOA are poorly understood. We isolated an ammonia-oxidizing archaeon (designated strain DDS1) from seawater and used this organism to study the physiology of ammonia oxidation. These findings were confirmed using four additional Thaumarchaeota strains from both marine and terrestrial habitats. Ammonia oxidation by strain DDS1 was enhanced in coculture with other bacteria, as well as in artificial seawater media supplemented with alpha-keto acids (e.g., pyruvate, oxaloacetate). alpha-Keto acid-enhanced activity of AOA has previously been interpreted as evidence of mixotrophy. However, assays for heterotrophic growth indicated that incorporation of pyruvate into archaeal membrane lipids was negligible. Lipid carbon atoms were, instead, derived from dissolved inorganic carbon, indicating strict autotrophic growth. alpha-Keto acids spontaneously detoxify H2O2 via a nonenzymatic decarboxylation reaction, suggesting a role of alpha-keto acids as H2O2 scavengers. Indeed, agents that also scavenge H2O2, such as dimethylthiourea and catalase, replaced the alpha-keto acid requirement, enhancing growth of strain DDS1. In fact, in the absence of alpha-keto acids, strain DDS1 and other AOA isolates were shown to endogenously produce H2O2 (up to similar to 4.5 mu M), which was inhibitory to growth. Genomic analyses indicated catalase genes are largely absent in the AOA. Our results indicate that AOA broadly feature strict autotrophic nutrition and implicate H2O2 as an important factor determining the activity, evolution, and community ecology of AOA ecotypes.</P>
Spindle-shaped viruses infect marine ammonia-oxidizing thaumarchaea
Kim, Jong-Geol,Kim, So-Jeong,Cvirkaite-Krupovic, Virginija,Yu, Woon-Jong,Gwak, Joo-Han,Ló,pez-Pé,rez, Mario,Rodriguez-Valera, Francisco,Krupovic, Mart,Cho, Jang-Cheon,Rhee, Sung-Keun National Academy of Sciences 2019 Proceedings of the National Academy of Sciences Vol.116 No.31
<P><B>Significance</B></P><P>Ammonia-oxidizing archaea (AOA) are major players in global nitrogen cycling. The physicochemical and metabolic factors affecting the composition of AOA communities and their efficiency of resource utilization have been studied extensively. However, viral predation on AOA remains unexplored due to lack of isolated virus–host systems. Here we report on the isolation and characterization of three <I>Nitrosopumilus</I> spindle-shaped viruses (NSVs) that infect AOA hosts. NSVs represent a potentially important group of marine viruses with a chronic infection cycle, providing important insights into the diversity and evolution of the archaeal virosphere. The wide spread of NSVs in AOA-containing marine environments suggests that NSV predation might regulate the diversity and dynamics of AOA communities, thereby affecting the carbon and nitrogen cycling.</P><P>Ammonia-oxidizing archaea (AOA) from the phylum Thaumarchaeota are ubiquitous in marine ecosystems and play a prominent role in carbon and nitrogen cycling. Previous studies have suggested that, like all microbes, thaumarchaea are infected by viruses and that viral predation has a profound impact on thaumarchaeal functioning and mortality, thereby regulating global biogeochemical cycles. However, not a single virus capable of infecting thaumarchaea has been reported thus far. Here we describe the isolation and characterization of three <I>Nitrosopumilus</I> spindle-shaped viruses (NSVs) that infect AOA and are distinct from other known marine viruses. Although NSVs have a narrow host range, they efficiently infect autochthonous <I>Nitrosopumilus</I> strains and display high rates of adsorption to their host cells. The NSVs have linear double-stranded DNA genomes of ∼28 kb that do not display appreciable sequence similarity to genomes of other known archaeal or bacterial viruses and could be considered as representatives of a new virus family, the “Thaspiviridae.” Upon infection, NSV replication leads to inhibition of AOA growth, accompanied by severe reduction in the rate of ammonia oxidation and nitrite reduction. Nevertheless, unlike in the case of lytic bacteriophages, NSV propagation is not associated with detectable degradation of the host chromosome or a decrease in cell counts. The broad distribution of NSVs in AOA-dominated marine environments suggests that NSV predation might regulate the diversity and dynamics of AOA communities. Collectively, our results shed light on the diversity, evolution, and potential impact of the virosphere associated with ecologically important mesophilic archaea.</P>
Ketobacter alkanivorans gen. nov., sp. nov., an n-alkane-degrading bacterium isolated from seawater
Kim, Seol-Hee,Kim, Jong-Geol,Jung, Man-Young,Kim, So-Jeong,Gwak, Joo-Han,Yu, Woon-Jong,Roh, Seong Woon,Kim, Yang-Hoon,Rhee, Sung-Keun Microbiology Society 2018 International journal of systematic and evolutiona Vol.68 No.7
Novel archaeal virus infecting marine ammonia-oxidizing thaumarchaea
Jong-Geol Kim 한국당과학회 2022 한국당과학회 학술대회 Vol.2022 No.07
Ammonia-oxidizing archaea (AOA) from the phylum Thaumarchaeota are ubiquitous in marine ecosystems and play an important role in the carbon and nitrogen cycling. Although viruses are known to have a key impact on the functioning and mortality of their hosts, thereby regulating the global biogeochemical cycles, not a single virus infecting thaumarchaea has been isolated thus far. Here we report on the isolation and characterization of the Nitrosopumilus spindle-shaped viruses (NSV) which infect a marine AOA and are distinct from other known marine viruses. Their morphology, genome architecture and life cycle indicate that they are distantly related to spindle-shaped viruses infecting hyperthermophilic and hyperhalophilic archaea. However, NSVs do not share appreciable sequence similarity to other archaeal viruses, except for the protein-primed family B DNA polymerase, and are likely to represent a new virus family. NSVs have high adsorption rate to host cells and are not lytic. These properties might be important for the predation on chemolithoautotrophic hosts in resource-poor environments. We show that NSV infection results in cessation of ammonia oxidation, although host cells are not lysed. Widespread distribution of NSV in marine sediments indicates that viral predation regulates the diversity and dynamics in the AOA community.