Habitat partitioning of denitrifying bacterial communities carrying nirS or nirK genes in the stratified water column of Lake Kinneret, Israel

Junier, Pilar; Kim, Ok-Sun; Witzel, Karl-Paul; Imhoff, Johannes F.; Hadas, Ora

doi:10.3354/ame01186

Cited by 19 publications

(34 citation statements)

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“…The total abundance of nirK denitrifiers may also vary spatially and temporally (Dandie et al 2008), and it has been reported to correlate with denitrification activity in stream sediments (O'Connor et al 2006). The nirS community was not addressed in the present study, due to technical problems in the nirS-DGGE, but it is possible that the response to environmental factors varies between nirK and nirS communities (Desnues et al 2007, Junier et al 2008, Enwall et al 2010, Kim et al 2011. A more complete picture of the denitrifier community could be acquired by concurrent analyses of nirS-containing communities and the total abundance of denitrification genes by qPCR.…”

Section: Discussionmentioning

confidence: 99%

Interlake variation and environmental controls of denitrification across different geographical scales

Rissanen¹,

Tiirola²,

Hietanen³

et al. 2013

Aquat. Microb. Ecol.

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Denitrification in lakes significantly reduces the nitrogen (N) load from land to oceans, but the factors controlling it remain poorly understood. Therefore, interlake variation of denitrification in sediments of small to medium-sized lakes (from 0.03 to 17.8 km 2 ) was studied across different geographical scales. At the local scale, the denitrification rates and sediment microbial communities were studied in 4 boreal lakes in close proximity (within 20 km) using the isotope pairing technique (IPT) and molecular methods. These local scale data were combined with previously published data on denitrification rates from 10 other European lakes to extend the analysis to the regional (boreal area) and continental (boreal and temperate areas) scales. Denitrification varied considerably among lakes, ranging from ~50 to ~600, ~0 to ~600 and ~0 to ~12900 µmol N m −2 d −1at the local, regional and continental scales, respectively. This variation was primarily due to nitrate availability. The structure of the denitrifier community studied at the local scale was independent of the denitrification rates but varied among lakes correlating with nitrate availability and sediment organic content. Removal of nitrate and total N load by denitrification was less efficient in boreal than in temperate lakes. In addition, a meta-analysis of published N mass balance data indicates that the total N retention (denitrification + N sedimentation) is less efficient in boreal than in temperate lakes. Anaerobic ammonium oxidation (anammox) was studied at the local scale but was not detected, although (based on molecular markers) several anammox genera were present in the sediments.KEY WORDS: Denitrification · Lake · Sediment · nirK Resale or republication not permitted without written consent of the publisherRemoval of nitrate and total N load by denitrification was less efficient in boreal than in temperate lakes. Photos: Ilpo Hakala (boreal) and Thyes (temperate)Aquat Microb Ecol 69: [1][2][3][4][5][6][7][8][9][10][11][12][13][14][15][16] 2013

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Section: Discussionmentioning

confidence: 99%

Interlake variation and environmental controls of denitrification across different geographical scales

Rissanen¹,

Tiirola²,

Hietanen³

et al. 2013

Aquat. Microb. Ecol.

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“…In a previous study on the community composition of denitrifying bacteria in Lake Kinneret (Israel), we have found that denitrifying bacteria carrying the nirK and nirS genes are differentially distributed in the stratified water column. In Lake Kinneret, communities of nirS-denitrifiers were diversified in the epilimnion and nirK-denitrifiers in the anoxic hypolimnion (Junier et al 2008b). …”

Section: Introductionmentioning

confidence: 97%

Distribution of denitrifying bacterial communities in the stratified water column and sediment–water interface in two freshwater lakes and the Baltic Sea

et al. 2010

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We have studied the distribution and community composition of denitrifying bacteria in the stratified water column and at the sediment-water interface in lakes Plußsee and Schöhsee, and a nearshore site in the Baltic Sea in Germany. Although environmental changes induced by the stratification of the water column in marine environments are known to affect specific populations of denitrifying bacteria, little information is available for stratified freshwater lakes and brackish water. The aim of the present study was to fill this gap and to demonstrate specific distribution patterns of denitrifying bacteria in specific aquatic habitats using two functional markers for the nitrite reductase (nirK and nirS genes) as a proxy for the communities. The leading question to be answered was whether communities containing the genes nirK and nirS have similar, identical, or different distribution patterns, and occupy the same or different ecological niches. The genes nirK and nirS were analyzed by PCR amplification with specific primers followed by terminal restriction fragment length polymorphism (T-RFLP) and by cloning and sequence analysis. Overall, nirS-denitrifiers were more diverse than nirK-denitrifiers. Denitrifying communities in sediments were clearly different from those in the water column in all aquatic systems, regardless of the gene analyzed. A differential distribution of denitrifying assemblages was observed for each particular site. In the Baltic Sea and Lake Plußsee, nirK-denitrifiers were more diverse throughout the water column, while nirSdenitrifiers were more diverse in the sediment. In Lake Schöhsee, nirS-denitrifiers showed high diversity across the whole water body. Habitat-specific clusters of nirS sequences were observed for the freshwater lakes, while nirK sequences from both freshwater lakes and the Baltic Sea were found in Handling Editor: Piet Spaak.Electronic supplementary material The online version of this article (common phylogenetic clusters. These results demonstrated differences in the distribution of bacteria containing nirS and those containing nirK indicating that both types of denitrifiers apparently occupy different ecological niches.

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“…However, 14 C bicarbonate uptake experiments that have been carried out for many years and in different seasons suggest that at the chemocline in autumn, when the oxycline and the thermocline are at the same depth within a narrow metalimnetic layer below the euphotic zone, sulfide oxidation is a much more significant process than ammonia oxidation (Hadas et al 2001). Although ammonia oxidation exists, and may be coupled to denitrification, as shown by amplification of the nitrite reductase gene nirS in the same samples (Junier et al 2008c), it is negligible during this period. In the lower part of the gradient, ammonia concentrations decrease from 14.2 µmol l -1 at 17.7 m to 6.3 µmol l -1 at 16.6 m depth, without the accumulation of nitrate and in the absence of amoA sequences in the libraries suggesting assimilation processes by metalimnetic biota rather than ammonia oxidation.…”

Section: Discussionmentioning

confidence: 99%

“…T-RFLP data were analyzed using GeneScan 3.1 software (Applied Biosystems). Data analysis was carried out as described in Junier et al (2008c). Simulations of terminal restriction fragments (T-RFs) from clonal sequences from this study were carried out using TRiFLe (Junier et al 2008a).…”

Section: Methodsmentioning

confidence: 99%

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Methane- and ammonia-oxidizing bacteria at the chemocline of Lake Kinneret (Israel)

Junier¹,

Kim²,

Eckert³

et al. 2010

Aquat. Microb. Ecol.

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The vertical distribution of methane- and ammonia-oxidizing bacteria (MOB and AOB, respectively), and the physicochemical conditions in the chemocline of Lake Kinneret (Israel) were studied at a resolution of 10 cm from 16.2 to 17.7 m depth. Profiles of the chemical parameters indicated decreasing concentrations of methane (from 22.4 to 0.11 µmol l–1) and ammonia (from 14.2 to 8.4 µmol l–1) towards the water surface and in close proximity to the chemocline. The disappearance of methane coincided with methane oxidation that could be corroborated throughout this layer with highest rates at 17.4 to 17.6 m. Disappearance of ammonia could not be linked to ammonia oxidation exclusively. The genes pmoA and the homologous amoA (coding for subunit α of the methane and ammonia monooxygenase, respectively) were amplified by PCR. The products were analyzed by terminal restriction fragment length polymorphism (T-RFLP) and sequencing of clone libraries. The results demonstrated that different MOB and AOB communities are established along the concentration gradient within the narrow layer of the metalimnetic chemocline. Changes in the intensity of the T-RFLP peaks and the frequency of different groups of alpha- and gammaproteobacterial MOB, and betaproteobacterial AOB, coincided with the concentration gradients of methane, ammonia, nitrate, and oxygen in the chemocline. This suggests that different communities of MOB, and to a lesser extent AOB, contribute to the formation of chemical gradients of their particular substrates in the chemocline

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Habitat partitioning of denitrifying bacterial communities carrying nirS or nirK genes in the stratified water column of Lake Kinneret, Israel

Cited by 19 publications

References 32 publications

Interlake variation and environmental controls of denitrification across different geographical scales

Interlake variation and environmental controls of denitrification across different geographical scales

Distribution of denitrifying bacterial communities in the stratified water column and sediment–water interface in two freshwater lakes and the Baltic Sea

Methane- and ammonia-oxidizing bacteria at the chemocline of Lake Kinneret (Israel)

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