Nitrification rates related to sedimentary structures in an Atlantic intertidal mudflat, Marennes-Oléron Bay, France

Laima, Mario; Girard, Michelle; Vouvé, Florence; Richard, Pierre; Blanchard, Gérard; Gouleau, Dominique

doi:10.3354/meps191033

Cited by 8 publications

(4 citation statements)

References 16 publications

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“…The experimental procedure involved incubation under anoxic atmosphere although surface sediment was oxidized. But the penetration of O 2 was small, about 2 mm depth (Laima et al, 1999), and influenced only slightly the rates.…”

Section: Kinetics Of Gross Ammonification and Nh 4 + Incorporationmentioning

confidence: 86%

“…For example, sediment surface temperature is likely to influence NH 4 + production and incorporation rates since it varies at several time scales: seasonally, fortnightly due to the tidal cycle and hourly due to the emersion period (Guarini et al, 1997). It is therefore necessary to quantify the relationship between NH 4 + production, incorporation rates and temperature -as well as the other N cycle processes, including nitrification (Laima et al, 1999) -to be able to model the dynamics of NH 4 + in intertidal sediments and thus the contribution of benthic regeneration to coastal productivity.…”

Section: Introductionmentioning

confidence: 99%

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NH4+ turnover in intertidal sediments of Marennes-Oléron Bay (France): effect of sediment temperature

et al. 2000

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NH 4 + turnover plays an important role in benthic compartment as source of nutrient for primary production. The intertidal mudflats of the Marennes-Oléron Bay are characterized by high fluctuations of sediment temperature that generally ranges from 10 to 30°C during emersion periods. Influence of sediment temperature on NH 4 + processes was investigated. Gross ammonification and NH 4 + incorporation kinetics were studied using the 15 N isotope dilution method. The method was first adapted to these very fine sediments and applied to 2 upper sediment layers (0 -2 and 2 -4 cm) at different incubation times of up to 120 h. The effect of sediment temperature on gross ammonification and NH 4 + incorporation rates was investigated at 10, 20 and 30°C. There was a strong increase of both rates as a function of temperature, gross ammonification rates ranged from 0 to 17 mg NH 4 + -N.g -1 dw.d -1 and NH 4 + incorporation rates from 2 to 13 mg N.g -1 dw.d -1 between 10 and 30°C. This study showed that short-term temperature variations during the emersion period should be taken into account in quantifying NH 4 + turnover in intertidal sediments and that benthic regeneration of NH 4 + significantly supports benthic and planktonic primary production in Marennes-Oléron Bay. It suggests also that there is no N-limitation for benthic primary production in this bay and that there is up to 44 % of NH 4 + produced in surface sediments, which can diffuse to the water column and become available to phytoplankton.

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Section: Kinetics Of Gross Ammonification and Nh 4 + Incorporationmentioning

confidence: 86%

Section: Introductionmentioning

confidence: 99%

NH4+ turnover in intertidal sediments of Marennes-Oléron Bay (France): effect of sediment temperature

et al. 2000

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“…The middle part of the bay, the Brouage mudflat, is characterized by the presence of flow-parallel sediment structures consisting of crests (ridges) and troughs (runnels). These side-by-side physical structures have been shown to significantly affect the nitrification rates (higher in runnels) ( 41 , 42 ). We ask if the physical structure of the ridges and runnels results in differences in the diversity of the nitrogen-cycling community present.…”

Section: Introductionmentioning

confidence: 99%

Ecological Observations Based on Functional Gene Sequencing Are Sensitive to the Amplicon Processing Method

Cholet

Lisik

Agogué

et al. 2022

mSphere

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Several analysis pipelines are available to microbial ecologists to process amplicon sequencing data, yet to date, there is no consensus as to the most appropriate method, and it becomes more difficult for genes that encode a specific function (functional genes). Standardized approaches need to be adopted to increase the reliability and reproducibility of environmental amplicon-sequencing-based data sets.

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“…The middle part of the bay, the Brouage mudflat, is characterized by the presence of flow-parallel sediment structures consisting of crests (ridges) and troughs (runnels). These side-by-side physical structures have been shown to significantly affect nitrification rates (higher in runnels) (37, 38). We ask if the physical structure of the ridges and runnels results in differences in the diversity of the nitrogen cycling community present.…”

Section: Introductionmentioning

confidence: 99%

Ecological Observations Based on Functional Gene Sequencing Are Sensitive to the Amplicon Processing Method

Cholet¹,

Lisik²,

Agogué³

et al. 2022

Preprint

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Until recently, the de-facto method for short read-based amplicons reconstruction is a sequence similarity threshold approach (Operational taxonomic Units OTUs). This assumption was relaxed by shifting to Amplicon Sequencing Variants (ASVs) where distributions are fitted to abundance profiles of individual genes using a noise-error model. Whilst OTUs-based approach is still useful for 16SrRNA/18S rRNA regions, where typically 97-99% thresholds are used, their utility to functional genes is still debatable as there is no consensus on how to cluster the sequences together. Here, we compare OTUs- and ASVs-based reconstruction approaches as well as taxonomy assignment methods, Naïve Bayesian Classifier (NBC) and Bayesian Lowest Common Ancestor Algorithm (BLCA), using functional genes dataset from the microbial nitrogen-cycling community in the Brouage mudflat (France). A range of OTU similarity thresholds and ASV were used to compare amoA (AOA and AOB), nxrB, nirS, nirK and nrfA communities between differing sedimentary structures. We show that for AOA-amoA and nrfA, the use of ASV led to differences in the communities between sedimentary structures whereas the use of OTUs didn’t. Conversely, significant differences were detected when using OTU (97%) for AOB-amoA but not with ASV or OTUs at other similarity thresholds. Interestingly, conclusions drawn from the other three functional genes were consistent between amplicon reconstruction methods. We also show that, when the sequences in the reference-database are related to the environment in question, BLCA leads to more phylogenetically relevant classifications. However, when the reference database contains sequences more dissimilar to the ones retrieved, NBC helps obtain more information.

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Nitrification rates related to sedimentary structures in an Atlantic intertidal mudflat, Marennes-Oléron Bay, France

Cited by 8 publications

References 16 publications

NH4+ turnover in intertidal sediments of Marennes-Oléron Bay (France): effect of sediment temperature

NH4+ turnover in intertidal sediments of Marennes-Oléron Bay (France): effect of sediment temperature

Ecological Observations Based on Functional Gene Sequencing Are Sensitive to the Amplicon Processing Method

Ecological Observations Based on Functional Gene Sequencing Are Sensitive to the Amplicon Processing Method

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