Limits...
Diversity and spatial distribution of hydrazine oxidoreductase (hzo) gene in the oxygen minimum zone off Costa Rica.

Kong L, Jing H, Kataoka T, Buchwald C, Liu H - PLoS ONE (2013)

Bottom Line: In this study, anammox bacterial communities in the OMZ off Costa Rica (CRD-OMZ) were analyzed based on both hydrazine oxidoreductase (hzo) genes and their transcripts assigned to cluster 1 and 2.Gene quantification results showed that hzo gene abundances peaked in the upper OMZs, associated with the peaks of nitrite concentration.A novel hzo cluster 2x clade was identified by the phylogenetic analysis and these novel sequences were abundant and widely distributed in this environment.

View Article: PubMed Central - PubMed

Affiliation: Division of Life Science, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong.

ABSTRACT
Anaerobic ammonia oxidation (anammox) as an important nitrogen loss pathway has been reported in marine oxygen minimum zones (OMZs), but the community composition and spatial distribution of anammox bacteria in the eastern tropical North Pacific (ETNP) OMZ are poorly determined. In this study, anammox bacterial communities in the OMZ off Costa Rica (CRD-OMZ) were analyzed based on both hydrazine oxidoreductase (hzo) genes and their transcripts assigned to cluster 1 and 2. The anammox communities revealed by hzo genes and proteins in CRD-OMZ showed a low diversity. Gene quantification results showed that hzo gene abundances peaked in the upper OMZs, associated with the peaks of nitrite concentration. Nitrite and oxygen concentrations may therefore colimit the distribution of anammox bacteria in this area. Furthermore, transcriptional activity of anammox bacteria was confirmed by obtaining abundant hzo mRNA transcripts through qRT-PCR. A novel hzo cluster 2x clade was identified by the phylogenetic analysis and these novel sequences were abundant and widely distributed in this environment. Our study demonstrated that both cluster 1 and 2 anammox bacteria play an active role in the CRD-OMZ, and the cluster 1 abundance and transcriptional activity were higher than cluster 2 in both free-living and particle-attached fractions at both gene and transcriptional levels.

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Location of sampling stations in Costa Rica Dome (CRD).
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pone-0078275-g001: Location of sampling stations in Costa Rica Dome (CRD).

Mentions: Sampling was conducted at three stations in the OMZ off Costa Rica coast during the FLUZiE cruise in June and July 2010 (Figure 1). No specific permissions were required for sampling in these locations. All of the three stations are located in the region of the Costa Rica Dome (CRD) with an annual mean thermocline depth of 35 and 40 m (20°C isotherm depth) according to previous study [37]. Seawater samples together with hydrographical data were collected by a conductivity-temperature-depth (CTD) rosette system (Sea-Bird Electronics) with attached Niskin bottles. The dissolved oxygen concentration was measured by a Seabird oxygen sensor attached to the CTD and the range of the OMZ was then determined. For DNA isolation, 1 liter seawater from four to eight depths inside and outside of the OMZs at each station was filtered onto a 2 μm and then a 0.2 μm pore size polycarbonate filter (47 mm, Millipore) with a low vacuum pressure. The same procedure was conducted for RNA sample collection, except that the filters were immersed in RNAlater solution (Ambion) immediately after the filtration. All of the filters were flash frozen and stored at -80°C until further analysis. Nitrite concentrations were measured on board using the Greiss-Ilosvay colorometric method on a UV-VIS spectrophotometer [42]. The ammonium samples were measured on board using a fluorometric method for low concentration samples described in Holmes et al. [43]. The detection limits for nitrite and ammonium concentrations were 0.1 and 0.03 μM, respectively.


Diversity and spatial distribution of hydrazine oxidoreductase (hzo) gene in the oxygen minimum zone off Costa Rica.

Kong L, Jing H, Kataoka T, Buchwald C, Liu H - PLoS ONE (2013)

Location of sampling stations in Costa Rica Dome (CRD).
© Copyright Policy
Related In: Results  -  Collection

Show All Figures
getmorefigures.php?uid=PMC3814345&req=5

pone-0078275-g001: Location of sampling stations in Costa Rica Dome (CRD).
Mentions: Sampling was conducted at three stations in the OMZ off Costa Rica coast during the FLUZiE cruise in June and July 2010 (Figure 1). No specific permissions were required for sampling in these locations. All of the three stations are located in the region of the Costa Rica Dome (CRD) with an annual mean thermocline depth of 35 and 40 m (20°C isotherm depth) according to previous study [37]. Seawater samples together with hydrographical data were collected by a conductivity-temperature-depth (CTD) rosette system (Sea-Bird Electronics) with attached Niskin bottles. The dissolved oxygen concentration was measured by a Seabird oxygen sensor attached to the CTD and the range of the OMZ was then determined. For DNA isolation, 1 liter seawater from four to eight depths inside and outside of the OMZs at each station was filtered onto a 2 μm and then a 0.2 μm pore size polycarbonate filter (47 mm, Millipore) with a low vacuum pressure. The same procedure was conducted for RNA sample collection, except that the filters were immersed in RNAlater solution (Ambion) immediately after the filtration. All of the filters were flash frozen and stored at -80°C until further analysis. Nitrite concentrations were measured on board using the Greiss-Ilosvay colorometric method on a UV-VIS spectrophotometer [42]. The ammonium samples were measured on board using a fluorometric method for low concentration samples described in Holmes et al. [43]. The detection limits for nitrite and ammonium concentrations were 0.1 and 0.03 μM, respectively.

Bottom Line: In this study, anammox bacterial communities in the OMZ off Costa Rica (CRD-OMZ) were analyzed based on both hydrazine oxidoreductase (hzo) genes and their transcripts assigned to cluster 1 and 2.Gene quantification results showed that hzo gene abundances peaked in the upper OMZs, associated with the peaks of nitrite concentration.A novel hzo cluster 2x clade was identified by the phylogenetic analysis and these novel sequences were abundant and widely distributed in this environment.

View Article: PubMed Central - PubMed

Affiliation: Division of Life Science, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong.

ABSTRACT
Anaerobic ammonia oxidation (anammox) as an important nitrogen loss pathway has been reported in marine oxygen minimum zones (OMZs), but the community composition and spatial distribution of anammox bacteria in the eastern tropical North Pacific (ETNP) OMZ are poorly determined. In this study, anammox bacterial communities in the OMZ off Costa Rica (CRD-OMZ) were analyzed based on both hydrazine oxidoreductase (hzo) genes and their transcripts assigned to cluster 1 and 2. The anammox communities revealed by hzo genes and proteins in CRD-OMZ showed a low diversity. Gene quantification results showed that hzo gene abundances peaked in the upper OMZs, associated with the peaks of nitrite concentration. Nitrite and oxygen concentrations may therefore colimit the distribution of anammox bacteria in this area. Furthermore, transcriptional activity of anammox bacteria was confirmed by obtaining abundant hzo mRNA transcripts through qRT-PCR. A novel hzo cluster 2x clade was identified by the phylogenetic analysis and these novel sequences were abundant and widely distributed in this environment. Our study demonstrated that both cluster 1 and 2 anammox bacteria play an active role in the CRD-OMZ, and the cluster 1 abundance and transcriptional activity were higher than cluster 2 in both free-living and particle-attached fractions at both gene and transcriptional levels.

Show MeSH