Article

Jayakumar A, O'Mullan GD, Naqvi SWA, Ward BB.. Denitrifying bacterial community composition changes associated with stages of denitrification in oxygen minimum zones. Microb Ecol 58: 350-362

Department of Geosciences, Guyot Hall, Princeton University, Princeton, NJ 08544, USA.
Microbial Ecology (Impact Factor: 3.12). 03/2009; 58(2):350-62. DOI: 10.1007/s00248-009-9487-y
Source: PubMed

ABSTRACT

Denitrification in the ocean is a major sink for fixed nitrogen in the global N budget, but the process is geographically restricted to a few oceanic regions, including three oceanic oxygen minimum zones (OMZ) and hemipelagic sediments worldwide. Here, we describe the diversity and community composition of microbes responsible for denitrification in the OMZ using polymerase chain reaction, sequence and fragment analysis of clone libraries of the signature genes (nirK and nirS) that encode the enzyme nitrite reductase, responsible for key denitrification transformation steps. We show that denitrifying assemblages vary in space and time and exhibit striking changes in diversity associated with the progression of denitrification from initial anoxia through nitrate depletion. The initial denitrifying assemblage is highly diverse, but succession on the scale of 3-12 days leads to a much less diverse assemblage and dominance by one or a few phylotypes. This progression occurs in the natural environment as well as in enclosed incubations. The emergence of dominants from a vast reservoir of rare types has implications for the maintenance of diversity of the microbial population and suggests that a small number of microbial dominants may be responsible for the greatest rates of transformations involving nitrous oxide and global fixed nitrogen loss. Denitrifying blooms, driven by a few types responding to episodic environmental changes and distributed unevenly in time and space, are consistent with the sampling effect model of diversity-function relationships. Canonical denitrification thus appears to have important parallels with both primary production and nitrogen fixation, which are typically dominated by regionally and temporally restricted blooms that account for a disproportionate share of these processes worldwide.

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    • "It features a shallow oxygen minimum zone (OMZ) at about 100 m depth with oxygen concentrations of about 60 µmol O 2 kg −1 (Brandt et al., 2015) and a deeper OMZ at approximately 300–600 m depth with oxygen concentrations up to 40 O 2 µmol kg −1 (Karstensen et al., 2008). However, eddies originating in the Mauritanian upwelling regime and propagating westward can harbor much lower oxygen concentrations (∼ 4 µmol O 2 kg −1 ; Karstensen et al., 2015), potentially enabling N-loss processes (Strous et al., 2006; Kartal et al., 2007; Jetten et al., 2009; Jayakumar et al., 2009). Those mesoscale eddies may transport nutrient loaded but relatively N-deficient waters to the surface (McGillicudy et al., 2003, 2007; Mathis et al., 2007). "
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    ABSTRACT: In open-ocean regions, as is the Eastern Tropical North Atlantic (ETNA), pelagic production is the main source of dissolved organic matter (DOM) and is affected by dissolved inorganic nitrogen (DIN) and phosphorus (DIP) concentrations. Changes in pelagic production under nutrient amendments were shown to also modify DOM quantity and quality. However, little information is available about the effects of nutrient variability on chromophoric (CDOM) and fluorescent (FDOM) DOM dynamics. Here we present results from two mesocosm experiments (“Varied P” and “Varied N”) conducted with a natural plankton community from the ETNA, where the effects of DIP and DIN supply onDOM optical properties were studied. CDOM accumulated proportionally to phytoplankton biomass during the experiments. Spectral slope decreased over time indicating accumulation of high molecular weight DOM. In Varied N, an additional CDOM portion, as a result of bacterial DOM reworking, was determined. It increased the CDOM fraction in DOC proportionally to the supplied DIN. The humic-like FDOM component (Comp.1) was produced by bacteria proportionally to DIN supply. The protein-like FDOM component (Comp.2) was released irrespectively to phytoplankton or bacterial biomass, but depended on DIP and DIN concentrations. Under high DIN supply, Comp.2 was removed by bacterial reworking, leading to an accumulation of humic-like Comp.1. No influence of nutrient availability on amino acid-like FDOM component in peptide form (Comp.3) was observed. Comp.3 potentially acted as an intermediate product during formation or degradation of Comp.2. Our findings suggest that changes in nutrient concentrations may lead to substantial responses in the quantity and quality of optically active DOM and, therefore, might bias results of the applied in situ optical techniques for an estimation of DOC concentrations in open-ocean regions.
    Full-text · Article · Dec 2015 · Biogeosciences
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    • "It features a shallow oxygen minimum zone (OMZ) at about 100 m depth with oxygen concentrations of about 60 µmol O 2 kg −1 (Brandt et al., 2015) and a deeper OMZ at approximately 300–600 m depth with oxygen concentrations up to 40 O 2 µmol kg −1 (Karstensen et al., 2008). However, eddies originating in the Mauritanian upwelling regime and propagating westward can harbor much lower oxygen concentrations (∼ 4 µmol O 2 kg −1 ; Karstensen et al., 2015), potentially enabling N-loss processes (Strous et al., 2006; Kartal et al., 2007; Jetten et al., 2009; Jayakumar et al., 2009). Those mesoscale eddies may transport nutrient loaded but relatively N-deficient waters to the surface (McGillicudy et al., 2003, 2007; Mathis et al., 2007). "
    [Show abstract] [Hide abstract]
    ABSTRACT: In open-ocean regions, as is the Eastern Tropical North Atlantic (ETNA), pelagic production is the main source of dissolved organic matter (DOM) and is affected by dissolved inorganic nitrogen (DIN) and phosphorus (DIP) concentrations. Changes in pelagic production under nutrient amendments were shown to also modify DOM quantity and quality. However, little information is available about the effects of nutrient variability on chromophoric (CDOM) and fluorescent (FDOM) DOM dynamics. Here we present results from two mesocosm experiments ("Varied P" and "Varied N") conducted with a natural plankton community from the ETNA, where the effects of DIP and DIN supply on DOM optical properties were studied. CDOM accumulated proportionally to phytoplankton biomass during the experiments. Spectral slope (S) decreased over time indicating accumulation of high molecular weight DOM. In Varied N, an additional CDOM portion, as a result of bacterial DOM reworking, was determined. It increased the CDOM fraction in DOC proportionally to the supplied DIN. The humic-like FDOM component (Comp.1) was produced by bacteria proportionally to DIN supply. The protein-like FDOM component (Comp.2) was released irrespectively to phytoplankton or bacterial biomass, but depended on DIP and DIN concentrations. Under high DIN supply, Comp.2 was removed by bacterial reworking, leading to an accumulation of humic-like Comp.1. No influence of nutrient availability on amino acid-like FDOM component in peptide form (Comp.3) was observed. Comp.3 potentially acted as an intermediate product during formation or degradation of Comp.2. Our findings suggest that changes in nutrient concentrations may lead to substantial responses in the quantity and quality of optically active DOM and, therefore, might bias results of the applied in situ optical techniques for an estimation of DOC concentrations in open-ocean regions.
    Full-text · Article · May 2015 · Biogeosciences Discussions
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    • "Thus, it appears that the nirS-type nitrite-reducing bacteria are more abundant than nirK-encoding bacteria in deepsea subseafloor sediments. On the other hand, it has been suggested that the diversity of nitrite reducers at a given location may be high during the initial stage of nitrite removal (high ratio of nitrate/nitrite), but lower in later stages of the process when most of the available nitrate/ nitrite is exhausted (Jayakumar et al., 2009). If this holds true for deep-ocean subseafloor sediments, more nitrite reducers are expected at site 401, where the nitrate/nitrite ratio was the highest among all sites in this study (Fig. 1). "

    Full-text · Dataset · Sep 2013
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