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Residence of habitat-specific anammox bacteria in the deep-sea subsurface sediments of the South China Sea: analyses of marker gene abundance with physical chemical parameters.

Hong YG, Li M, Cao H, Gu JD - Microb. Ecol. (2011)

Bottom Line: Results indicated that the anammox bacterial sequences recovered from this habitat by amplifying both 16S rRNA gene and hydrazine oxidoreductase encoding hzo gene were all closely related to the Candidatus Scalindua genus.A total of 96 16S rRNA gene sequences from 346 clones were grouped into five subclusters: two subclusters affiliated with the brodae and arabica species, while three new subclusters named zhenghei-I, -II, and -III showed ≤ 97.4% nucleic acid sequence identity with other known Candidatus Scalindua species.Meanwhile, 88 hzo gene sequences from the sediments also formed five distant subclusters within hzo cluster 1c.

View Article: PubMed Central - PubMed

Affiliation: Key Laboratory of Tropical Marine Environment Dynamics (LED), South China Sea Institute of Oceanography, Chinese Academy of Sciences, Guangzhou, 510301, People's Republic of China.

ABSTRACT
Anaerobic ammonium oxidation (anammox) has been recognized as an important process for the global nitrogen cycle. In this study, the occurrence and diversity of anammox bacteria in the deep-sea subsurface sediments of the South China Sea (SCS) were investigated. Results indicated that the anammox bacterial sequences recovered from this habitat by amplifying both 16S rRNA gene and hydrazine oxidoreductase encoding hzo gene were all closely related to the Candidatus Scalindua genus. A total of 96 16S rRNA gene sequences from 346 clones were grouped into five subclusters: two subclusters affiliated with the brodae and arabica species, while three new subclusters named zhenghei-I, -II, and -III showed ≤ 97.4% nucleic acid sequence identity with other known Candidatus Scalindua species. Meanwhile, 88 hzo gene sequences from the sediments also formed five distant subclusters within hzo cluster 1c. Through fluorescent real-time PCR analysis, the abundance of anammox bacteria in deep-sea subsurface sediment was quantified by hzo genes, which ranged from 1.19 × 10(4) to 7.17 × 10(4) copies per gram of dry sediments. Combining all the information from this study, diverse Candidatus Scalindua anammox bacteria were found in the deep-sea subsurface sediments of the SCS, and they could be involved in the nitrogen loss from the fixed inventory in the habitat.

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Phylogenetic tree based on an alignment of 16S rRNA gene sequences showing the phylogenetic affiliations of anammox bacterial sequences from the different subseafloor sediment of South China Sea. The numbers in parentheses refer to how many clones retrieved by the amplification with the primer sets Brod541F/Amx820R and Amx368/ Amx820R were assigned to an individual phylotype. The consensus phylogenetic tree constructed based on neighbor-joining analysis. The numbers at the nodes are percentages that indicate the levels of bootstrap support based on 500 resampled data sets. Branch lengths correspond to sequence differences as indicated by the scale bar
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Fig1: Phylogenetic tree based on an alignment of 16S rRNA gene sequences showing the phylogenetic affiliations of anammox bacterial sequences from the different subseafloor sediment of South China Sea. The numbers in parentheses refer to how many clones retrieved by the amplification with the primer sets Brod541F/Amx820R and Amx368/ Amx820R were assigned to an individual phylotype. The consensus phylogenetic tree constructed based on neighbor-joining analysis. The numbers at the nodes are percentages that indicate the levels of bootstrap support based on 500 resampled data sets. Branch lengths correspond to sequence differences as indicated by the scale bar

Mentions: The phylogenetic tree was built with the 96 positive anammox clones and other known anammox 16S rRNA gene sequences using neighbor-joining and maximum parsimony algorithms (Fig. 1). The tree revealed that all anammox bacterial-like sequences of this study were affiliated with the genus Candidatus Scalindua. Two phylogenetic trees constructed using different algorithms supported the grouping of anammox bacterial sequences into six coherent subclusters: brodae subcluster, arabica subcluster, wagneri subcluster, zhenghei-I subcluster, zhenghei-II subcluster, and zhenghei-III subcluster. The 96 anammox-like sequences identified from the deep-sea subsurface sediments of SCS were distributed into five of the six subclusters; none of the sequences that were identified were affiliated with the wagneri group. The percentage of anammox-like sequences affiliated with the brodae subcluster was 62.5%. This subcluster includes sequences from all four sampling sites. In addition, this subcluster contains identified anammox bacteria Candidatus Scalindua brodae, Candidatus Scalindua sorokinii as well as some clones from Peruvian and Namibian OMZs. Only one clone from the E525 sampling site was included within the arabica subcluster, which is a newly proposed anammox bacteria phylotype [56].Figure 1


Residence of habitat-specific anammox bacteria in the deep-sea subsurface sediments of the South China Sea: analyses of marker gene abundance with physical chemical parameters.

Hong YG, Li M, Cao H, Gu JD - Microb. Ecol. (2011)

Phylogenetic tree based on an alignment of 16S rRNA gene sequences showing the phylogenetic affiliations of anammox bacterial sequences from the different subseafloor sediment of South China Sea. The numbers in parentheses refer to how many clones retrieved by the amplification with the primer sets Brod541F/Amx820R and Amx368/ Amx820R were assigned to an individual phylotype. The consensus phylogenetic tree constructed based on neighbor-joining analysis. The numbers at the nodes are percentages that indicate the levels of bootstrap support based on 500 resampled data sets. Branch lengths correspond to sequence differences as indicated by the scale bar
© Copyright Policy
Related In: Results  -  Collection

Show All Figures
getmorefigures.php?uid=PMC3141849&req=5

Fig1: Phylogenetic tree based on an alignment of 16S rRNA gene sequences showing the phylogenetic affiliations of anammox bacterial sequences from the different subseafloor sediment of South China Sea. The numbers in parentheses refer to how many clones retrieved by the amplification with the primer sets Brod541F/Amx820R and Amx368/ Amx820R were assigned to an individual phylotype. The consensus phylogenetic tree constructed based on neighbor-joining analysis. The numbers at the nodes are percentages that indicate the levels of bootstrap support based on 500 resampled data sets. Branch lengths correspond to sequence differences as indicated by the scale bar
Mentions: The phylogenetic tree was built with the 96 positive anammox clones and other known anammox 16S rRNA gene sequences using neighbor-joining and maximum parsimony algorithms (Fig. 1). The tree revealed that all anammox bacterial-like sequences of this study were affiliated with the genus Candidatus Scalindua. Two phylogenetic trees constructed using different algorithms supported the grouping of anammox bacterial sequences into six coherent subclusters: brodae subcluster, arabica subcluster, wagneri subcluster, zhenghei-I subcluster, zhenghei-II subcluster, and zhenghei-III subcluster. The 96 anammox-like sequences identified from the deep-sea subsurface sediments of SCS were distributed into five of the six subclusters; none of the sequences that were identified were affiliated with the wagneri group. The percentage of anammox-like sequences affiliated with the brodae subcluster was 62.5%. This subcluster includes sequences from all four sampling sites. In addition, this subcluster contains identified anammox bacteria Candidatus Scalindua brodae, Candidatus Scalindua sorokinii as well as some clones from Peruvian and Namibian OMZs. Only one clone from the E525 sampling site was included within the arabica subcluster, which is a newly proposed anammox bacteria phylotype [56].Figure 1

Bottom Line: Results indicated that the anammox bacterial sequences recovered from this habitat by amplifying both 16S rRNA gene and hydrazine oxidoreductase encoding hzo gene were all closely related to the Candidatus Scalindua genus.A total of 96 16S rRNA gene sequences from 346 clones were grouped into five subclusters: two subclusters affiliated with the brodae and arabica species, while three new subclusters named zhenghei-I, -II, and -III showed ≤ 97.4% nucleic acid sequence identity with other known Candidatus Scalindua species.Meanwhile, 88 hzo gene sequences from the sediments also formed five distant subclusters within hzo cluster 1c.

View Article: PubMed Central - PubMed

Affiliation: Key Laboratory of Tropical Marine Environment Dynamics (LED), South China Sea Institute of Oceanography, Chinese Academy of Sciences, Guangzhou, 510301, People's Republic of China.

ABSTRACT
Anaerobic ammonium oxidation (anammox) has been recognized as an important process for the global nitrogen cycle. In this study, the occurrence and diversity of anammox bacteria in the deep-sea subsurface sediments of the South China Sea (SCS) were investigated. Results indicated that the anammox bacterial sequences recovered from this habitat by amplifying both 16S rRNA gene and hydrazine oxidoreductase encoding hzo gene were all closely related to the Candidatus Scalindua genus. A total of 96 16S rRNA gene sequences from 346 clones were grouped into five subclusters: two subclusters affiliated with the brodae and arabica species, while three new subclusters named zhenghei-I, -II, and -III showed ≤ 97.4% nucleic acid sequence identity with other known Candidatus Scalindua species. Meanwhile, 88 hzo gene sequences from the sediments also formed five distant subclusters within hzo cluster 1c. Through fluorescent real-time PCR analysis, the abundance of anammox bacteria in deep-sea subsurface sediment was quantified by hzo genes, which ranged from 1.19 × 10(4) to 7.17 × 10(4) copies per gram of dry sediments. Combining all the information from this study, diverse Candidatus Scalindua anammox bacteria were found in the deep-sea subsurface sediments of the SCS, and they could be involved in the nitrogen loss from the fixed inventory in the habitat.

Show MeSH