Quantification of ammonia oxidizing bacteria in soil using microcolony technique combined with fluorescence in situ hybridization (MCFU–FISH)

Hesselsøe, Martin

doi:10.1016/s0168-6496(01)00187-8

Cited by 37 publications

(29 citation statements)

References 29 publications

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“…The relationship between activity and AOB abundance is consistent with the correlations obtained between nitrification levels and the abundance of cultivable AOB at the same study sites under field conditions (Patra et al, 2005). Similarly, strong correlations were obtained between nitrification and the abundance of AOB assessed by qPCR in salt marsh sediments (Dollhopf et al, 2005), among various soil depths in arable cropping systems (Berg and Rosswall, 1987), and in soil amended with or without ammonium (Hesselsøe et al, 2001) (but see Mendum et al, 1999;Phillips et al, 2000a;Wheatley et al, 2003). Whereas some data have been available on the expected behavior of AOB, almost no results have been published so far on abundance of AOA in grassland soils and possible interaction with grazing.…”

Section: G -G V S U -Usupporting

confidence: 85%

Effects of aboveground grazing on coupling among nitrifier activity, abundance and community structure

et al. 2007

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The influence of switches in grassland management to or from grazing on the dynamics of nitrifier activity, as well as the abundance of ammonia-oxidizing bacteria, AOB and ammonia-oxidizing archeae, AOA, was analyzed for two years after changing management. Additionally community structure of AOB was surveyed. Four treatments were compared in mesocosms: grazing on previously grazed grassland (G-G); no grazing on ungrazed grassland (U-U); grazing on ungrazed grassland (U-G) and cessation of grazing on grazed grassland (G-U). Nitrifier activity and abundance were always higher for G-G than U-U treatments and AOB community structure differed between these treatments. AOA abundance was in the same range as AOB abundance and followed the same trend. Grazing led to a change in AOB community structure within o5 months and a subsequent (5-12 months) increase in nitrifier activity and abundance. In contrast, cessation of grazing led to a decrease in nitrifier activity and abundance within o5 months and to a later (5-12 months) change in AOB community structure. Activity in G-U and U-G was similar to that in U-U and G-G, respectively, after 12 months. Sequence analysis of 16S rRNA gene clones showed that AOB retrieved from soils fell within the Nitrosospira lineage and percentages of AOB related to known Nitrosospira groups were affected by grazing. These results demonstrate that AOB and AOA respond quickly to changes in management. The selection of nitrifiers adapted to novel environmental conditions was a prerequisite for nitrification enhancement in U-G, whereas nitrification decrease in G-U was likely due to a partial starvation and decrease in the abundance of nitrifiers initially present. The results also suggest that taxonomic affiliation does not fully infer functional traits of AOB.

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Section: G -G V S U -Usupporting

confidence: 85%

Effects of aboveground grazing on coupling among nitrifier activity, abundance and community structure

et al. 2007

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“…A prerequisite is that the extraction efficiency is preferably high, but at least similar, in the soils under comparison. Since the reporting cell population is inoculated only shortly (1 h) in the soil under the standard assay conditions, a rather high extraction efficiency may be expected, as is typically found for microbial inocula, including N. europaea (1,21). Based on the optimization experiments for the soil extract protocol, bioluminescence was only slightly lower in the soil extracts than in pure culture with the same amount of inoculum (Fig.…”

Section: Vol 68 2002 Bioluminescent N Europaea Reporter Of Las Toxmentioning

confidence: 88%

“…which occur more commonly in soil (9,29,30). Alternatively, indigenous AOB are mostly sessile (1,21) and the surface-associated cells could be less exposed to the LAS amendment or represent different cell types with a higher LAS tolerance. We propose that the solid phase-contact assay with the reporter strain N. europaea ATCC 19718(pHLUX20) is more sensitive in measuring the toxicity effects of soil pollutants than the commonly used assay of potential ammonia oxidation activity.…”

Section: Vol 68 2002 Bioluminescent N Europaea Reporter Of Las Toxmentioning

confidence: 99%

Solid-Phase Contact Assay That Uses alux-MarkedNitrosomonas europaeaReporter Strain To Estimate Toxicity of Bioavailable Linear Alkylbenzene Sulfonate in Soil

Brandt¹,

Pedersen²,

Sørensen³

2002

Appl Environ Microbiol

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Information about in situ toxicity of the bioavailable pools of adsorptive soil pollutants is a prerequisite for proper ecological risk assessment in contaminated soils. Such toxicity data may be obtained by assays allowing for direct exposure of introduced test microorganisms to the toxicants, as they appear in solid solution equilibria in the natural soil. We describe a novel sensitive solid-phase contact assay for in situ toxicity testing of soil pollutants based on a recombinant bioluminescent reporter strain of Nitrosomonas europaea. A slurry of the reporter strain and soil sample was shaken for 1 h, after which bioluminescence was measured either directly (soil slurry protocol) or in the supernatant obtained after centrifugation (soil extract protocol). The assay was validated for both protocols by using linear alkylbenzene sulfonate (LAS) as a toxic and adsorptive model compound in the soil samples. Interestingly, LAS showed the same toxicity to the reporter strain with either soil incubation (both protocols) or pure culture, suggesting that adsorbed LAS pools contributed to the observed toxicity. The solid-phase contact assay that used the reporter strain of lux-marked N. europaea was slightly more sensitive for the detection of LAS toxicity in soil than activity-based assays targeting indigenous nitrifiers and much more sensitive than assays targeting indigenous heterotrophic microbes. We conclude that the new solid-phase contact assay, which is based on direct interaction of the test microorganisms with bioavailable pools of the toxicants in soil, provides a most sensitive and relevant method for evaluating the in situ toxicity and assessing the risks of soil contaminants.

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“…Mobarry et al (1996) has reported that Nso l90 and Nso 1225 encompass all sequenced ammonia oxidizers of the ␣ subclass of Proteobacteria. However, some investigations showed that there was a sequence mismatch between the probe sequence (both Nsol90 and Nso1225) and the target sequence of the bacteria of one or a few bases (Purkhold et al, 2000;Hesselsoe et al, 2001;Persson et al, 2002). So, in this study NSO190 together with NSO1225 was applied to investigate the population dynamics of ammonia oxidizers.…”

Section: Fish Analysismentioning

confidence: 99%

Nitrification performance and microbial community dynamics in a submerged membrane bioreactor with complete sludge retention

Yang

Zhang

et al. 2006

Journal of Biotechnology

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A submerged membrane bioreactor (MBR) supplied with inorganic ammonium-bearing wastewater (NH 4 + -N, 500 mg l −1 ) was operated for 260 days without sludge purge under decreased hydraulic retention times (HRT) through six steps (from 30 to 5 h). Almost complete nitrification was obtained at a volumetric loading rate (VLR) 1.2 g NH 4 + -N l −1 day −1 . The sludge nitrification activities were evaluated at each stage. The specific ammonium oxidizing rate (SAOR) decreased from the initial 0.45 to 0.15 kg NH 4 + -N kg −1 MLSS day −1 in the last four stages, while the specific nitrate forming rate (SNFR) increased from 0.17 to 0.39 kg NO 3 − -N kg −1 MLSS day −1 at the third stage, and then decreased to below 0.1 kg NO 3from the fourth stage. Microbial population dynamics was investigated by a combination of the MPN method, fluorescence in situ hybridization (FISH) and quinone profiles. During the experiment, although the MLSS increased gradually from 4.5 to 11.5 g l −1 , the number of ammonia-oxidizing bacteria (AOB) decreased from 10 9 l −1 at the third stage to 10 7 l −1 in the last two stages, and that of nitrite-oxidizing bacteria (NOB) decreased gradually from 10 8 l −1 at the second stage (HRT of 20 h) to the final 10 5 l −1 . FISH results showed that the active cells decreased gradually with time from about 60 to 20% in the last two stages, and most of sludge was inert cells. The sum of nitrifiers occupied only about 10% of the total bacteria number in the last stage even though only ammonium-bearing inorganic wastewater was fed in. Nitrosomonas sp. and Nitrospira sp. were confirmed by FISH as the dominant nitrifying genera responsible for ammonia and nitrite oxidation, respectively. In the mean time, a small ratio of Nitrobacter sp. also existed in the system. FISH analysis matched better with the batch activity test results than did the MPN techniques. Quinone profiles revealed that the dominant ubiquinone was ubiquinone-8 (UQ-8), ranging from 84 to 66%, followed by UQ-10 of 7-13%, UQ-7 of 3-5% and UQ-9 of 1.6-2.6%. The dominant menaquinone in the MBR was menaquinone-7 (MK-7) followed by MK-6, MK-8 and MK-8 (H 2 ). With the prolongation of operation, the percentage of menaquinones increased from 8 to 14%. The use of the polyphasic approach gave some new insight on variations of microbial community structures.

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Quantification of ammonia oxidizing bacteria in soil using microcolony technique combined with fluorescence in situ hybridization (MCFU–FISH)

Cited by 37 publications

References 29 publications

Effects of aboveground grazing on coupling among nitrifier activity, abundance and community structure

Effects of aboveground grazing on coupling among nitrifier activity, abundance and community structure

Solid-Phase Contact Assay That Uses alux-MarkedNitrosomonas europaeaReporter Strain To Estimate Toxicity of Bioavailable Linear Alkylbenzene Sulfonate in Soil

Nitrification performance and microbial community dynamics in a submerged membrane bioreactor with complete sludge retention

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