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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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Neighbor-joining phylogenetic tree constructed with anammox bacteria hzo-deduced amino acid sequences from the oxygen minimum zone (OMZ) in Costa Rica Dome (CRD).The sequences in bold were obtained in the present study. The sequences were grouped at a 1% cutoff value using DOTUR and only one sequence was selected to represent the operational taxonomic unit (OTU). The number in the brackets followed the sequence name indicated the number of the clones recovered. Bootstrap resampling was performed 1000 times and only its values higher than 50% are shown. The scale bar presents the number of amino acid substitutions per site.
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pone-0078275-g004: Neighbor-joining phylogenetic tree constructed with anammox bacteria hzo-deduced amino acid sequences from the oxygen minimum zone (OMZ) in Costa Rica Dome (CRD).The sequences in bold were obtained in the present study. The sequences were grouped at a 1% cutoff value using DOTUR and only one sequence was selected to represent the operational taxonomic unit (OTU). The number in the brackets followed the sequence name indicated the number of the clones recovered. Bootstrap resampling was performed 1000 times and only its values higher than 50% are shown. The scale bar presents the number of amino acid substitutions per site.

Mentions: In contrast to the highly similar community compositions in each gene cluster, lower hzo (57.0-59.4%) and HZO (45.2-47.1%) sequence similarities were shared between cluster 1 and cluster 2, and they were separated into two distinct clades in the phylogenetic tree (Figure 4). The topology of phylogenetic tree was supported by different algorithms of maximum parsimony and neighbor joining methods. The obtained HZO cluster 1 sequences were affiliated into the Candidatus Scalindua clade. Although the obtained cluster 2 sequences were amplified with the primers previously designed for hzo cluster 2a, they were distinct (< 60% of amino acid sequence similarity) from the existing cluster 2a sequences and any other known HZO sequences in the database, therefore we named them hzo cluster 2x clade in our study.


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)

Neighbor-joining phylogenetic tree constructed with anammox bacteria hzo-deduced amino acid sequences from the oxygen minimum zone (OMZ) in Costa Rica Dome (CRD).The sequences in bold were obtained in the present study. The sequences were grouped at a 1% cutoff value using DOTUR and only one sequence was selected to represent the operational taxonomic unit (OTU). The number in the brackets followed the sequence name indicated the number of the clones recovered. Bootstrap resampling was performed 1000 times and only its values higher than 50% are shown. The scale bar presents the number of amino acid substitutions per site.
© Copyright Policy
Related In: Results  -  Collection

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

pone-0078275-g004: Neighbor-joining phylogenetic tree constructed with anammox bacteria hzo-deduced amino acid sequences from the oxygen minimum zone (OMZ) in Costa Rica Dome (CRD).The sequences in bold were obtained in the present study. The sequences were grouped at a 1% cutoff value using DOTUR and only one sequence was selected to represent the operational taxonomic unit (OTU). The number in the brackets followed the sequence name indicated the number of the clones recovered. Bootstrap resampling was performed 1000 times and only its values higher than 50% are shown. The scale bar presents the number of amino acid substitutions per site.
Mentions: In contrast to the highly similar community compositions in each gene cluster, lower hzo (57.0-59.4%) and HZO (45.2-47.1%) sequence similarities were shared between cluster 1 and cluster 2, and they were separated into two distinct clades in the phylogenetic tree (Figure 4). The topology of phylogenetic tree was supported by different algorithms of maximum parsimony and neighbor joining methods. The obtained HZO cluster 1 sequences were affiliated into the Candidatus Scalindua clade. Although the obtained cluster 2 sequences were amplified with the primers previously designed for hzo cluster 2a, they were distinct (< 60% of amino acid sequence similarity) from the existing cluster 2a sequences and any other known HZO sequences in the database, therefore we named them hzo cluster 2x clade in our study.

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