Article

Denitrifying bacterial community composition changes associated with stages of denitrification in oxygen minimum zones.

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.

0 Bookmarks
 · 
92 Views
  • [Show abstract] [Hide abstract]
    ABSTRACT: The organization of denitrifying microorganisms in oil-polluted bioturbated sediments was investigated in mesocosms under conditions as closer as possible to that observed in the environment. Molecular and culture-dependent approaches revealed that denitrifying Gammaproteobacteria were abundant in oil-polluted and bioturbated sediments suggesting that they may play a key role in hydrocarbon degradation in the environment. T-RFLP and gene libraries analyses targeting nirS gene showed that denitrifying microbial communities structure was slightly affected by either the addition of Hediste diversicolor or crude oil revealing the metabolic versatility of denitrifying microorganisms. From oil-polluted sediments, distinct denitrifying hydrocarbonoclastic bacterial consortia were obtained by enrichment cultures on high molecular weight PAHs (dibenzothiophene, fluoranthene, pyrene and chrysene) under nitrate-reducing conditions. Interestingly, molecular characterization of the consortia showed that the denitrifying communities obtained from oiled microcosms with addition of H. diversicolor were different to that observed without H. diversicolor addition, especially with fluoranthene and chrysene revealing the bacterial diversity involved in the degradation of these PAHs. This article is protected by copyright. All rights reserved.
    FEMS Microbiology Ecology 05/2014; 89(3). DOI:10.1111/1574-6941.12359 · 3.88 Impact Factor
  • Source
    [Show abstract] [Hide abstract]
    ABSTRACT: The Northeastern Arabian Sea (NEAS) is a recognized region of intense denitrification, with a 200 to 1200 m anoxic water column. We studied the abundance of bacteria, viral particles and the bacterial community (BC), in addition to various chemical and other biological parameters from the Arabian Sea Time Series (ASTS) station. Water samples from surface, deep chlorophyll maximum (DCM), 250, 500 and 1000 m were collected during spring intermonsoon (SIM), fall intermonsoon (FIM), and northeast monsoon (NEM) seasons and analyzed for various parameters. Bacterial abundance varied seasonally (p ≤ 0.05), with the highest abundance observed during FIM at all sampling depths. Conversely, seasonal variations in viral abundance were minimal, though a significant correlation between viral and bacterial abundance (r = 0.526, p < 0.05, n = 14) was found. Hierarchical clustering of denaturing gradient gel electrophoresis (DGGE) profiles revealed clear patterns of vertical, as well as temporal, partitioning of the BC during all 3 seasons. The BC varied seasonally both in the surface and DCM, whereas in the oxygen minimum zone (OMZ; 250 to 1000 m) it was more or less identical during all 3 seasons in spite of significant seasonal variation in bacterial abundance, pH and dissolved oxygen (DO) levels in the OMZ. Following band-matching, several DGGE bands were excised and sequenced. Phylogenetic analysis of these sequences revealed Alphaproteobacteria, Gammaproteobacteria, and Cyanobacteria as the dominant bacterial groups at the ASTS location. Linkage tree (LINKTREE) and canonical correspondence analysis (CCA) were performed to decipher the effect of environmental factors on the BC. From these analyses, it appears that DO and total organic carbon (TOC) are responsible for vertical separation of the BC between the surface and the OMZ. Our results suggest seasonal variation in the BC occurs in the surface layers, with minimal temporal differences in the OMZ.
    Aquatic Microbial Ecology 08/2014; 73(1):51-67. DOI:10.3354/ame01704 · 1.90 Impact Factor
  • Source

Full-text (3 Sources)

Download
59 Downloads
Available from
May 15, 2014