A Mesophilic, Autotrophic, Ammonia-Oxidizing Archaeon of Thaumarchaeal Group I.1a Cultivated from a Deep Oligotrophic Soil Horizon

Jung, Man‐Young; Park, Soo-Je; Kim, So-Jeong; Kim, Jong-Geol; Damsté, Jaap S. Sinninghe; Jeon, Che Ok; Rhee, Sung‐Keun

doi:10.1128/aem.03730-13

Cited by 78 publications

(57 citation statements)

References 72 publications

(119 reference statements)

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“…The second most abundant archaea in the sediment of the two creeks belonged to Thaumarchaeota. These previous studies indicated that Thaumarchaeota have been linked to methanogenic activities and ammonia oxidation in the environment [89,90]. The relative abundance of Methanobacteria was slightly higher in the sediment of the industry creek than that of the sewage creek.…”

Section: Discussionmentioning

confidence: 97%

Effect of Sewage and Industrial Effluents on Bacterial and Archaeal Communities of Creek Sediments in the Taihu Basin

Xia

Wang

et al. 2017

Water

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Different characteristics of wastewater have different effects on the diversity and abundance of bacteria and archaea in rivers. There are many creeks around Taihu Lake, and they receive a large volume of industrial wastewater and domestic sewage, which is discharged into these creeks, and finally into Taihu Lake. The present study determined Illumina reads (16S rRNA gene amplicons) to analyze the effects of industrial wastewater and domestic sewage on the bacterial and archaeal communities at the different sampling sites along two creeks. The bacterial and archaeal diversity of the creek receiving sewage was higher than that of the creek receiving industrial waste. Proteobacteria dominated the microbial communities of all samples in both creeks. Betaproteobacteria dominated in the sewage creek, and its abundance declined along the creek. Certain pollutant-resistant classes were more abundant at the site near to the pollution source of the industry creek (e.g., Epsilonproteobacteria and Flavobacteria). Halobacteria belonging to the phylum Euryarchaeota was the dominant archaea at all sites in both creeks, while Methanobacteria was more abundant in the industry creek. The bacterial community was more affected by the distance between the sampling site and the pollutant source than the archaeal community, indicating that bacterial diversity and abundance could be a good index to distinguish domestic and industrial pollution, especially when the main pollution sources are difficult to identify.

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Section: Discussionmentioning

confidence: 97%

Effect of Sewage and Industrial Effluents on Bacterial and Archaeal Communities of Creek Sediments in the Taihu Basin

Xia

Wang

et al. 2017

Water

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“…This traditional viewpoint was thoroughly challenged and changed on the basis of the discovery of AOA. So far, more than 10 strains of AOA were already isolated, and more than 10 enrichments have been cultivated (Blainey et al, 2011;De La Torre et al, 2008;Elling et al, 2015;Hallam et al, 2006;Hatzenpichler et al, 2008;Jung et al, 2011;Jung et al, 2014;Kim et al, 2012;Kim et al, 2016;Könneke et al, 2005;Lehtovirta-Morley et al, 2011;Lehtovirta-Morley et al, 2016a;Mosier et al, 2012;Qin et al, 2014;Sauder et al, 2017). Yet more than 80% of the AOA were still undiscovered so far (Biller et al, 2012).…”

Section: Introductionmentioning

confidence: 99%

Potential correlated environmental factors leading to the niche seg- regation of ammonia-oxidizing archaea and ammonia-oxidizing bac- teria: A review

Liu¹,

Hu²,

Shen³

et al. 2017

Appl Env Biotechnol

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Ammonia oxidation is an important step of the nitrogen cycle and was considered to be conducted only by ammonia-oxidizing bacteria (AOB) for a long time. The discovery of ammonia-oxidizing archaea (AOA) caused consideration of the relative contributions of these two functional groups in different niches and factors resulting in their niche segregation. Previous studies showed that some environmental factors may correlate to the abundance and distribution of AOA and AOB, including ammonia/ammonium concentration, pH, organic matters, oxygen concentration, temperature, salinity, sulfide concentration, phosphate concentration, soil moisture and so on. Despite extensive studies conducted on ecology of AOA and AOB to find key environmental factors dominating niche segregation between AOA and AOB, few studies were conducted to explore the interrelationship among environmental factors. In this review, five main environmental factors which may be related to each other were selectively reviewed independently, including ammonia concentration, pH, temperature, oxygen concentration and organic matters. Furthermore, potential interrelationship among environmental factors was proposed.

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“…These ammonia-oxidizing archaea are highly abundant in nature and contribute significantly to nitrification as well as to primary production in marine, terrestrial, and geothermal environments (2)(3)(4)(5)(6)(7)(8)(9)(10)(11). Nitrosopumilus maritimus, the first cultured thaumarchaeon, may be regarded as a model organism since it has served to unravel characteristic cellular, genomic, and physiological features of this group (12)(13)(14)(15)(16).…”

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confidence: 99%

Malonic Semialdehyde Reductase from the Archaeon Nitrosopumilus maritimus Is Involved in the Autotrophic 3-Hydroxypropionate/4-Hydroxybutyrate Cycle

Otte

Mall

Schubert

et al. 2015

Appl Environ Microbiol

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The recently described ammonia-oxidizing archaea of the phylum Thaumarchaeota are highly abundant in marine, geothermal, and terrestrial environments. All characterized representatives of this phylum are aerobic chemolithoautotrophic ammonia oxidizers assimilating inorganic carbon via a recently described thaumarchaeal version of the 3-hydroxypropionate/4-hydroxybutyrate cycle. Although some genes coding for the enzymes of this cycle have been identified in the genomes of Thaumarchaeota, many other genes of the cycle are not homologous to the characterized enzymes from other species and can therefore not be identified bioinformatically. Here we report the identification and characterization of malonic semialdehyde reductase Nmar_1110 in the cultured marine thaumarchaeon Nitrosopumilus maritimus. This enzyme, which catalyzes the reduction of malonic semialdehyde with NAD(P)H to 3-hydroxypropionate, belongs to the family of iron-containing alcohol dehydrogenases and is not homologous to malonic semialdehyde reductases from Chloroflexus aurantiacus and Metallosphaera sedula. It is highly specific to malonic semialdehyde (K m , 0.11 mM; V max , 86.9 mol min ؊1 mg ؊1 of protein) and exhibits only low activity with succinic semialdehyde (K m , 4.26 mM; V max , 18.5 mol min ؊1 mg ؊1 of protein). Homologues of N. maritimus malonic semialdehyde reductase can be found in the genomes of all Thaumarchaeota sequenced so far and form a well-defined cluster in the phylogenetic tree of iron-containing alcohol dehydrogenases. We conclude that malonic semialdehyde reductase can be regarded as a characteristic enzyme for the thaumarchaeal version of the 3-hydroxypropionate/4-hydroxybutyrate cycle.A ll cultured members of a recently described archaeal phylum, Thaumarchaeota (1), are chemolithoautotrophs which aerobically oxidize ammonia to nitrite (2). These ammonia-oxidizing archaea are highly abundant in nature and contribute significantly to nitrification as well as to primary production in marine, terrestrial, and geothermal environments (2-11). Nitrosopumilus maritimus, the first cultured thaumarchaeon, may be regarded as a model organism since it has served to unravel characteristic cellular, genomic, and physiological features of this group (12)(13)(14)(15)(16). N. maritimus couples ammonia oxidation at extremely low ammonia concentrations (of low nanomolar range) to autotrophic CO 2 fixation (14). Chemolithotrophic life in extremely nutrient-limited environments results in a permanently low energy supply and requires special metabolic adaptation to enable growth. Indeed, CO 2 fixation, the central anabolic process in autotrophs, proceeds in N. maritimus via a novel variant of the 3-hydroxypropionate/ 4-hydroxybutyrate (HP/HB) cycle, which represents the most energy-efficient aerobic autotrophic pathway (13). Genes of this HP/HB cycle were found in all thaumarchaeal genomes, indicating the potential operation in all members of the phylum Thaumarchaeota ( Fig. 1) and its ecological significance in various habitats (13).The HP...

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A Mesophilic, Autotrophic, Ammonia-Oxidizing Archaeon of Thaumarchaeal Group I.1a Cultivated from a Deep Oligotrophic Soil Horizon

Cited by 78 publications

References 72 publications

Effect of Sewage and Industrial Effluents on Bacterial and Archaeal Communities of Creek Sediments in the Taihu Basin

Effect of Sewage and Industrial Effluents on Bacterial and Archaeal Communities of Creek Sediments in the Taihu Basin

Potential correlated environmental factors leading to the niche seg- regation of ammonia-oxidizing archaea and ammonia-oxidizing bac- teria: A review

Malonic Semialdehyde Reductase from the Archaeon Nitrosopumilus maritimus Is Involved in the Autotrophic 3-Hydroxypropionate/4-Hydroxybutyrate Cycle

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