Estimation of Nitrifying Bacterial Activities by Measuring Oxygen Uptake in the Presence of the Metabolic Inhibitors Allylthiourea and Azide

Ginestet, P.; Audic, J. M.; Urbain, V.; Block, Jean-Claude

doi:10.1128/aem.64.6.2266-2268.1998

Cited by 203 publications

(90 citation statements)

References 19 publications

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“…We observed varied levels of inhibition in the presence of ATU at levels known to completely inhibit cultivated AOB (Ginestet et al, 1998). The presence of significant nitrification in the presence of ATU is consistent with only partial inhibition of AOA, such as Nitrososphaera gargensis, a moderately thermophilic ammonia-oxidizing archaeon (Hatzenpichler et al, 2008), and indicates that reliance on ATU for complete inhibition of nitrification may be unreliable.…”

Section: Nitrification Rates and Relevance To Euphotic Zone No 3dynamicssupporting

confidence: 52%

Activity, abundance and diversity of nitrifying archaea and bacteria in the central California Current

Santoro¹,

Casciotti²,

Francis³

2010

Environmental Microbiology

361

376

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A combination of stable isotope and molecular biological approaches was used to determine the activity, abundance and diversity of nitrifying organisms in the central California Current. Using (15)NH(4)(+) incubations, nitrification was detectable in the upper water column down to 500 m; maximal rates were observed just below the euphotic zone. Crenarchaeal and betaproteobacterial ammonia monooxygenase subunit A genes (amoA), and 16S ribosomal RNA (rRNA) genes of Marine Group I Crenarchaeota and a putative nitrite-oxidizing genus, Nitrospina, were quantified using quantitative PCR. Crenarchaeal amoA abundance ranged from three to six genes ml(-1) in oligotrophic surface waters to > 8.7 x 10(4) genes ml(-1) just below the core of the California Current at 200 m depth. Bacterial amoA abundance was lower than archaeal amoA and ranged from below detection levels to 400 genes ml(-1). Nitrification rates were not directly correlated to bacterial or archaeal amoA abundance. Archaeal amoA and Marine Group I crenarchaeal 16S rRNA gene abundances were correlated with Nitrospina 16S rRNA gene abundance at all stations, indicating that similar factors may control the distribution of these two groups. Putatively shallow water-associated archaeal amoA types ('Cluster A') decreased in relative abundance with depth, while a deep water-associated amoA type ('Cluster B') increased with depth. Although some Cluster B amoA sequences were found in surface waters, expressed amoA gene sequences were predominantly from Cluster A. Cluster B amoA transcripts were detected between 100 and 500 m depths, suggesting an active role in ammonia oxidation in the mesopelagic. Expression of marine Nitrosospira-like bacterial amoA genes was detected throughout the euphotic zone down to 200 m. Natural abundance stable isotope ratios (delta(15)N and delta(18)O) in nitrate (NO(3)(-)) and nitrous oxide (N(2)O) were used to evaluate the importance of nitrification over longer time scales. Using an isotope mass balance model, we calculate that nitrification could produce between 0.45 and 2.93 micromol m(-2) day(-1) N(2)O in the central California Current, or approximately 1.5-4 times the local N(2)O flux from deep water.

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Section: Nitrification Rates and Relevance To Euphotic Zone No 3dynamicssupporting

confidence: 52%

Activity, abundance and diversity of nitrifying archaea and bacteria in the central California Current

Santoro¹,

Casciotti²,

Francis³

2010

Environmental Microbiology

361

376

View full text Add to dashboard Cite

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“…Therefore, the rate of N 2 O accumulation over time after inhibition with acetylene in all the experiments corresponded to N 2 O produced by denitrification (N 2 Opd). ATU, an NH z 4 oxidation inhibitor (Ginestet et al 1998), was used to evaluate net N 2 O cycling of denitrification (net N 2 Od), which equaled production minus consumption by denitrifiers. Thus, the rate of N 2 O consumed by denitrification (N 2 Ocd) was estimated from the rates measured in experiments with acetylene (N 2 Opd) minus those quantified in the ATU experiment (under natural O 2 conditions).…”

Section: Methodsmentioning

confidence: 99%

Denitrification and nitrous oxide cycling within the upper oxycline of the eastern tropical South Pacific oxygen minimum zone

et al. 2009

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One of the shallowest, most intense oxygen minimum zones (OMZs) is found in the eastern tropical South Pacific, off northern Chile and southern Peru. It has a strong oxygen gradient (upper oxycline) and high N 2 O accumulation. N 2 O cycling by heterotrophic denitrification along the upper oxycline was studied by measuring N 2 O production and consumption rates using an improved acetylene blockage method.

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“…In Col. 3 (HCO 3 − ) and Col. 4 (H 13 CO 3 − ), ATU was used to suppress bacterial ammonia oxidation while feeding at the same NH 4 + loading as in Col. 1 and 2 (26). Complete inhibition of bacterial ammonia oxidation with ATU has been previously observed at ATU concentrations of 8-86 μM (37), while archaeal ammonia oxidation is less sensitive to ATU (38). The mechanism of ATU inhibition in AOB is proposed to be chelation of the Cu 2+ from the active site in the AMO enzyme (24).…”

Section: Resultsmentioning

confidence: 91%

DNA and RNA-SIP revealNitrospira spp.as key drivers of nitrification in groundwater-fed biofilters

Gülay

Fowler

Tatari

et al. 2019

Preprint

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20Nitrification, the oxidative process converting ammonia to nitrite and nitrate, is driven by microbes 21 and plays a central role in the global nitrogen cycle. Our earlier metagenomics, amoA-amplicon, and 22 amoA-qPCR based investigations of groundwater-fed biofilters indicated a consistently high 23 abundance of comammox Nitrospira, and we hypothesized that these non-classical nitrifiers drive 24 ammonia-N oxidation. Hence, we used DNA and RNA stable isotope probing (SIP) coupled with 25 16S rRNA amplicon sequencing to identify the active members in the biofilter community when 26 subject to a continuous supply of NH4 + or NO2in the presence of 13 C-HCO3 -(labelled) or 12 C-HCO3 -27 (unlabelled). Allylthiourea (ATU) and sodium chlorate were added to inhibit autotrophic ammonia-28 and nitrite-oxidizing bacteria, respectively. Our results confirmed that lineage II Nitrospira 29 dominated ammonium oxidation in the biofilter community. A total of 78 (8 in RNA-SIP and 70 in 30 DNA-SIP) and 96 (25 in RNA-SIP and 71 in DNA-SIP) Nitrospira phylotypes (at 99% 16S rRNA 31 sequence similarity) were identified as complete ammonia-and nitrite-oxidizing, respectively. We 32 also detected significant HCO3uptake by Acidobacteria subgroup10, Pedomicrobium, Rhizobacter, 33 and Acidovorax under conditions that favoured ammonium oxidation. Canonical Nitrospira alone 34 drove nitrite oxidation in the biofilter community, and activity of archaeal ammonia oxidizing taxa 35 was not detected in the SIP fractions. This study provides the first in-situ evidence of ammonia 36 oxidation by comammox Nitrospira in an ecologically relevant complex microbiome. 38Nitrification, the stepwise oxidation of ammonia (NH3) to nitrite (NO2 -) and nitrate (NO3 -), supplies 40 the substrates for processes that initiate the loss of reactive nitrogen from the biosphere as N2. 41 Understanding the organisms and environmental controls that drive nitrification is important as it 42 controls global homeostasis of the N cycle. In engineered environments, complete nitrification is 43 often desired: this is essential when waters are prepared and distributed for human consumption. 44 Residual NH3 or NO2 --the result of incomplete nitrification -renders the water biologically unstable 45 and unsafe for human consumption. Hence, biological systems for source water treatment are 46 contingent on nitrifying prokaryotes. Based on evolutionarily conserved taxonomic (small subunit, 47 16S rRNA) and functional (e.g. ammonia monooxygenase, amoA) gene surveys, Nitrosomonas (1-48 4), Nitrosoarchaeum, and Nitrososphaera have been identified as the abundant ammonium oxidizing 49 prokaryotes (AOP) and Nitrospira (5, 6) as the abundant nitrite oxidizing prokaryotes (NOP) in 50 drinking water treatment systems, consistent with the classical assumption of division of labor in the 51 two nitrification steps. 52Our previous studies on rapid gravity sand filters (RGSF), used in potable water preparation from 53 groundwater, revealed nitrifying microbial communi...

show abstract

Estimation of Nitrifying Bacterial Activities by Measuring Oxygen Uptake in the Presence of the Metabolic Inhibitors Allylthiourea and Azide

Cited by 203 publications

References 19 publications

Activity, abundance and diversity of nitrifying archaea and bacteria in the central California Current

Activity, abundance and diversity of nitrifying archaea and bacteria in the central California Current

Denitrification and nitrous oxide cycling within the upper oxycline of the eastern tropical South Pacific oxygen minimum zone

DNA and RNA-SIP revealNitrospira spp.as key drivers of nitrification in groundwater-fed biofilters

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