Enrichment and Characterization of an Autotrophic Ammonia-Oxidizing Archaeon of Mesophilic Crenarchaeal Group I.1a from an Agricultural Soil

Jung, Man‐Young; Park, Soo-Je; Min, Dongbo; Kim, Jin-Seog; Rijpstra, W. Irene C.; Damsté, Jaap S. Sinninghe; Kim, Geun-Joong; Madsen, Eugene L.; Rhee, Sung‐Keun

doi:10.1128/aem.05787-11

Cited by 242 publications

(255 citation statements)

References 104 publications

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“…Strains of soil ammonia-oxidizing archaea (AOA) in the clade Thaumarchaeota, which were cultivated in laboratories, were shown to be capable of growing as autotrophic ammonia oxidizers (Jung et al, 2011;Lehtovirta-Morley et al, 2011;Kim et al, 2012). The thaumarchaeotal I.1a, I.1a-associated and I.1b clades are frequently recognized as the dominant ammonia-oxidizing organisms in terrestrial environments, possibly because of their high affinity for NH 3 (Jung et al, 2011;Kim et al, 2012).…”

Section: Introductionmentioning

confidence: 99%

Isotopic signatures of N2O produced by ammonia-oxidizing archaea from soils

Well²,

et al. 2013

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N 2 O gas is involved in global warming and ozone depletion. The major sources of N 2 O are soil microbial processes. Anthropogenic inputs into the nitrogen cycle have exacerbated these microbial processes, including nitrification. Ammonia-oxidizing archaea (AOA) are major members of the pool of soil ammonia-oxidizing microorganisms. This study investigated the isotopic signatures of N 2 O produced by soil AOA and associated N 2 O production processes. All five AOA strains (I.1a, I.1a-associated and I.1b clades of Thaumarchaeota) from soil produced N 2 O and their yields were comparable to those of ammonia-oxidizing bacteria (AOB). The levels of site preference (SP), d 15 N bulk and d 18 O -N 2 O of soil AOA strains were 13-30%, À 13 to À 35% and 22-36%, respectively, and strains MY1-3 and other soil AOA strains had distinct isotopic signatures. A 15 N-NH 4 þ -labeling experiment indicated that N 2 O originated from two different production pathways (that is, ammonia oxidation and nitrifier denitrification), which suggests that the isotopic signatures of N 2 O from AOA may be attributable to the relative contributions of these two processes. The highest N 2 O production yield and lowest site preference of acidophilic strain CS may be related to enhanced nitrifier denitrification for detoxifying nitrite. Previously, it was not possible to detect N 2 O from soil AOA because of similarities between its isotopic signatures and those from AOB. Given the predominance of AOA over AOB in most soils, a significant proportion of the total N 2 O emissions from soil nitrification may be attributable to AOA.

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Section: Introductionmentioning

confidence: 99%

Isotopic signatures of N2O produced by ammonia-oxidizing archaea from soils

Well²,

et al. 2013

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“…Nitrification-related processes (the oxidation of NH 2 OH and NO 2 − reduction) mediated by AOB are recognised to be a main pathway of N 2 O emission from arable soils (G dde and Conrad 1999;Zhu et al 2013;Huang et al 2014a). The traditional viewpoint that soil ammonia oxidation and associated N 2 O emission is exclusively carried out by AOB has been challenged by the discovery of amoA and nirK genes in AOA strains (Venter et al 2004;Lund et al 2012) and by the demonstration of the N 2 O production capacity of AOA enriched or isolated from arable soils and marine ecosystem (Jung et al 2011(Jung et al , 2014Santoro et al 2011;Loscher et al 2012). In most soils, AOA outnumbers AOB abundance, a common feature in multiple ecosystems (Leininger et al 2006;He et al 2007;Hu et al 2013), and a high AOA ammonia oxidation activity has been assessed in certain soils (Yao et al 2011;Zhang et al 2012;Hu et al 2015).…”

Section: Introductionmentioning

confidence: 99%

Nitrogen fertiliser-induced changes in N2O emissions are attributed more to ammonia-oxidising bacteria rather than archaea as revealed using 1-octyne and acetylene inhibitors in two arable soils

et al. 2016

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Nitrification is believed to be one of the major sources of N 2 O production emitted from soil. Previous studies showed that both ammonia-oxidising bacteria (AOB) and archaea (AOA) can produce N 2 O via nitrification but their relative contributions are still poorly defined. Here, we used acetylene, an inhibitor of AOB and AOA ammonia monooxygenase (AMO), and 1-octyne, a selective inhibitor that specifically inhibits AOB AMO, to investigate how AOB versus AOA contribute to N 2 O emissions in two distinct arable soils. Soil amended with ammonium (NH 4 + ) increased N 2 O emissions to a greater extent than nitrate (NO 3 − ), and acetylene had a greater impact on N 2 O emissions in NH 4 + -treated soils than that in NO 3 − -amended soils, which indicated that nitrification was the dominant N 2 O emitting process in these two arable soils. In the alluvial and red soil, the percentage of evolved N 2 O after application of NH 4 + by AOB were 70.5~78.1 % and 18.7~19.7 % by AOA, respectively. Quantitative PCR revealed that NH 4 + addition stimulated AOB growth, and the growth could be significantly inhibited by acetylene or 1-octyne in the two soils. The stimulation of N 2 O emissions by NH 4 + and the relative suppression by inhibitors paralleled fluctuations in the AOB growth. In addition, cumulative N 2 O emissions were not correlated with AOA abundance in the two soils. Our results revealed that AOB could contribute more to soil N 2 O production than AOA in the NH 4 + -amended arable soils.

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“…대섭이굴의 1.1a-Associated 그룹은 크게 두 개의 소그룹으로 세분화됨을 알 수 있었다. 또한 암모니아를 산화하는 고세균 그룹 중 하나인 I.1a 그룹의 염기서 열이 약 27%를 차지하고 있었다 (Jung et al, 2011). 정량 PCR을 …”

Section: )와 가장 가까운 근연관계가 있음을 확인할 수 있었다(16sunclassified

A Unique Prokaryotic Assemblage of Wall Biofilm of a Volcanic Cave (Daesubee) in Jeju

Moon¹,

Jung²,

Kim³

et al. 2013

The Korean Journal of Microbiology

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Cave environment provides special ecosystems for evolution of lives distant from surface environments. We investigated bacterial and archaeal communities of wall biofilm obtained from of a volcanic cave (Daesubee) in Jeju, Republic of Korea. Bacterial and archaeal 16S rRNA genes were PCR-amplified and sequenced using pyrosequencing technologies. Unique prokaryotic communities with low diversities were observed. The main bacterial sequences (ca. 83% of total reads) were affiliated with Pseudonocardia mongoliensis of phylum Actinobacteria and clustered with clones obtained from various caves. Reflection of light on the wall surface of cave might be caused by formation of beads of water caused by hydrophobic filaments of actinobacterial colonies. Main archaeal sequences (ca. 65.7% of total reads) were related with those of I.1a-Associated group of phylum Thaumarchaeota. The sequences were related with that of Candidatus Nitrosotalea devanaterra which was known to oxidize ammonia under acidic condition (ca. pH 5.0). Nutrients leached through volcanic soils contribute formation of unique microbial communities of wall biofilm of cave Daesubee.

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Enrichment and Characterization of an Autotrophic Ammonia-Oxidizing Archaeon of Mesophilic Crenarchaeal Group I.1a from an Agricultural Soil

Cited by 242 publications

References 104 publications

Isotopic signatures of N2O produced by ammonia-oxidizing archaea from soils

Isotopic signatures of N2O produced by ammonia-oxidizing archaea from soils

Nitrogen fertiliser-induced changes in N2O emissions are attributed more to ammonia-oxidising bacteria rather than archaea as revealed using 1-octyne and acetylene inhibitors in two arable soils

A Unique Prokaryotic Assemblage of Wall Biofilm of a Volcanic Cave (Daesubee) in Jeju

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