Nitrite oxidation kinetics of two Nitrospira strains: The quest for competition and ecological niche differentiation

Ushiki, Norisuke; Jinno, Masaru; Fujitani, Hirotsugu; Suenaga, Toshikazu; Terada, Akihiko; Tsuneda, Satoshi

doi:10.1016/j.jbiosc.2016.12.016

Cited by 100 publications

(69 citation statements)

References 42 publications

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“…When controlled for population size, NO 2 − kinetics followed the Michaelis‐Menten relationship. The half‐saturation constant ( K s = 0.254 ± 0.161 μM; average of two experiments, Figure ) was 1–3 orders of magnitude lower than that of pure cultures of three cultivated NOB genera ( Nitrobacter , Nitrotoga , and Nitrospira; K s = 6–544 μM) [ Blackburne et al , ; Nowka et al , ; Ushiki et al , ]. [NO 2 − ] accumulates to μM levels in OMZs, suggesting that the K s for NO 2 − might be even lower in regions with lower [NO 2 − ].…”

Section: Discussionmentioning

confidence: 99%

“…When controlled for population size, NO 2 À kinetics followed the Michaelis-Menten relationship. The halfsaturation constant (K s = 0.254 ± 0.161 μM; average of two experiments, Figure 2) was 1-3 orders of magnitude lower than that of pure cultures of three cultivated NOB genera (Nitrobacter, Nitrotoga, and Nitrospira; K s = 6-544 μM) [Blackburne et al, 2007;Nowka et al, 2015;Ushiki et al, 2017] [Oshiki et al, 2016]. Anammox cannot be the major pathway of apparently anaerobic NO 2 À oxidaton reported here, because measured rates of anammox in this region [Babbin, 2014] and in other OMZs [Hamersley et al, 2007;Dalsgaard et al, 2012;Babbin et al, 2014] are much lower (by tenfold) than the NO 2 À oxidation rates reported here.…”

Section: Effect Of No 2 à On No 2 à Oxidation Ratementioning

confidence: 94%

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Dependence of nitrite oxidation on nitrite and oxygen in low‐oxygen seawater

Sun

Jayakumar

et al. 2017

Geophysical Research Letters

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Nitrite oxidation is an essential step in transformations of fixed nitrogen. The physiology of nitrite oxidizing bacteria (NOB) implies that the rates of nitrite oxidation should be controlled by concentration of their substrate, nitrite, and the terminal electron acceptor, oxygen. The sensitivities of nitrite oxidation to oxygen and nitrite concentrations were investigated using 15N tracer incubations in the Eastern Tropical North Pacific. Nitrite stimulated nitrite oxidation under low in situ nitrite conditions, following Michaelis‐Menten kinetics, indicating that nitrite was the limiting substrate. The nitrite half‐saturation constant (Ks = 0.254 ± 0.161 μM) was 1–3 orders of magnitude lower than in cultivated NOB, indicating higher affinity of marine NOB for nitrite. The highest rates of nitrite oxidation were measured in the oxygen depleted zone (ODZ), and were partially inhibited by additions of oxygen. This oxygen sensitivity suggests that ODZ specialist NOB, adapted to low‐oxygen conditions, are responsible for apparently anaerobic nitrite oxidation.

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Section: Discussionmentioning

confidence: 99%

Section: Effect Of No 2 à On No 2 à Oxidation Ratementioning

confidence: 94%

Dependence of nitrite oxidation on nitrite and oxygen in low‐oxygen seawater

Sun

Jayakumar

et al. 2017

Geophysical Research Letters

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“…According to Blackburne and colleagues, Nitrospira had an inhibition threshold for free ammonia between 0.04 and 0.08 mg of NH 3 -N · liter Ϫ1 (41). Furthermore, a recent study based on Nitrospira isolates demonstrated that the nitrite oxidation activity of Nitrospira strains ND1 and NJ1 was inhibited at concentrations above 0.85 and 4.3 mg of NH 3 -N · liter Ϫ1 , respectively (42). With respect to thermophilic NOB related to Nitrospira calida derived from a nutrient-rich composting fertilizer, its sensitivity for free ammonia was lower than those of other reported Nitrospira spp., characterized by half-maximal inhibition of 5.0 mg of NH 3 -N · liter Ϫ1 (43).…”

Section: Discussionmentioning

confidence: 99%

Enrichment and Physiological Characterization of a Cold-Adapted Nitrite-Oxidizing Nitrotoga sp. from an Eelgrass Sediment

Fujitani

Soh

Nakagawa

et al. 2017

Appl Environ Microbiol

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Nitrite-oxidizing bacteria (NOB) are responsible for the second step of nitrification in natural and engineered ecosystems. The recently discovered genus Nitrotoga belongs to the Betaproteobacteria and potentially has high environmental importance. Although environmental clones affiliated with Nitrotoga are widely distributed, the limited number of cultivated Nitrotoga spp. results in a poor understanding of their ecophysiological features. In this study, we successfully enriched the nonmarine cold-adapted Nitrotoga sp. strain AM1 from coastal sand in an eelgrass zone and investigated its physiological characteristics. Multistep-enrichment approaches led to an increase in the abundance of AM1 to approximately 80% of the total bacterial population. AM1 was the only detectable NOB in the bacterial community. The 16S rRNA gene sequence of AM1 was 99.6% identical to that of "Candidatus Nitrotoga arctica," which was enriched from permafrost-affected soil. The highest nitrogen oxidation rate of AM1 was observed at 16°C. The half-saturation constant (K m ) and the generation time were determined to be 25 M NO 2 Ϫ and 54 h, respectively. The nitrite oxidation rate of AM1 was stimulated at concentrations of Ͻ30 mM NH 4 Cl but completely inhibited at 50 mM NH 4 Cl. AM1 can grow well under specific environmental conditions, such as low temperature and in the presence of a relatively high concentration of free ammonia. These results help improve our comprehension of the functional importance of Nitrotoga.IMPORTANCE Nitrite-oxidizing bacteria (NOB) are key players in the second step of nitrification, which is an important process of the nitrogen cycle. Recent studies have suggested that the organisms of the novel NOB genus Nitrotoga were widely distributed and played a functional role in natural and engineered ecosystems. However, only a few Nitrotoga enrichments have been obtained, and little is known about their ecology and physiology. In this study, we successfully enriched a Nitrotoga sp. from sand in a shallow coastal marine ecosystem and undertook a physiological characterization. The laboratory experiments showed that the Nitrotoga enrichment culture could adapt not only to low temperature but also to relatively high concentrations of free ammonia. The determination of as-yet-unknown unique characteristics of Nitrotoga contributes to the improvement of our insights into the microbiology of nitrification.KEYWORDS Nitrospira, Nitrotoga, ammonia, coastal sand, cultivation, enrichment, microbial communities, nitrification, nitrite-oxidizing bacteria, physiology I n nitrification, ammonia is oxidized into nitrate via nitrite by phylogenetically different chemolithoautotrophic microorganisms, and this is an integral part of the global nitrogen cycle. The reactions are catalyzed by ammonia-oxidizing bacteria (AOB),

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“…For details on the modules, see main text. Ammonia and nitrite K M values were taken from Kits et al (2017), Nowka et al (2015a), and Ushiki et al (2017)…”

Section: Potential Niche-defining Differences Between Strict Ammonia mentioning

confidence: 99%

Complete nitrification: insights into the ecophysiology of comammox Nitrospira

Koch

Kessel

Lücker

2018

Appl Microbiol Biotechnol

276

148

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Nitrification, the oxidation of ammonia via nitrite to nitrate, has been considered to be a stepwise process mediated by two distinct functional groups of microorganisms. The identification of complete nitrifying Nitrospira challenged not only the paradigm of labor division in nitrification, it also raises fundamental questions regarding the environmental distribution, diversity, and ecological significance of complete nitrifiers compared to canonical nitrifying microorganisms. Recent genomic and physiological surveys identified factors controlling their ecology and niche specialization, which thus potentially regulate abundances and population dynamics of the different nitrifying guilds. This review summarizes the recently obtained insights into metabolic differences of the known nitrifiers and discusses these in light of potential functional adaptation and niche differentiation between canonical and complete nitrifiers.Electronic supplementary materialThe online version of this article (10.1007/s00253-018-9486-3) contains supplementary material, which is available to authorized users.

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Nitrite oxidation kinetics of two Nitrospira strains: The quest for competition and ecological niche differentiation

Cited by 100 publications

References 42 publications

Dependence of nitrite oxidation on nitrite and oxygen in low‐oxygen seawater

Dependence of nitrite oxidation on nitrite and oxygen in low‐oxygen seawater

Enrichment and Physiological Characterization of a Cold-Adapted Nitrite-Oxidizing Nitrotoga sp. from an Eelgrass Sediment

Complete nitrification: insights into the ecophysiology of comammox Nitrospira

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