Limits...
amoA-encoding archaea and thaumarchaeol in the lakes on the northeastern Qinghai-Tibetan Plateau, China.

Yang J, Jiang H, Dong H, Wang H, Wu G, Hou W, Liu W, Zhang C, Sun Y, Lai Z - Front Microbiol (2013)

Bottom Line: The results showed that the archaeal amoA gene was present in hypersaline lakes with salinity up to 160 g L(-) (1).Thaumarchaeol was present in all of the studied hypersaline lakes, even in those where no AEA amoA gene was observed.Future research is needed to determine the ecological function of AEA and possible sources of thaumarchaeol in the Qinghai-Tibetan hypersaline lakes.

View Article: PubMed Central - PubMed

Affiliation: State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences Wuhan, China ; Key Lab of Salt Lake Resources and Chemistry, Qinghai Institute of Salt Lakes, Chinese Academy of Sciences Xining, China.

ABSTRACT
All known ammonia-oxidizing archaea (AOA) belong to the phylum Thaumarchaeota within the domain Archaea. AOA possess the diagnostic amoA gene (encoding the alpha subunit of ammonia monooxygenase) and produce lipid biomarker thaumarchaeol. Although the abundance and diversity of amoA gene-encoding archaea (AEA) in freshwater lakes have been well-studied, little is known about AEA ecology in saline/hypersaline lakes. In this study, the distribution of the archaeal amoA gene and thaumarchaeol were investigated in nine Qinghai-Tibetan lakes with a salinity range from freshwater to salt-saturation (salinity: 325 g L(-) (1)). The results showed that the archaeal amoA gene was present in hypersaline lakes with salinity up to 160 g L(-) (1). The archaeal amoA gene diversity in Tibetan lakes was different from those in other lakes worldwide, suggesting Tibetan lakes (high elevation, strong ultraviolet, and dry climate) may host a unique AEA population of different evolutionary origin from those in other lakes. Thaumarchaeol was present in all of the studied hypersaline lakes, even in those where no AEA amoA gene was observed. Future research is needed to determine the ecological function of AEA and possible sources of thaumarchaeol in the Qinghai-Tibetan hypersaline lakes.

No MeSH data available.


Related in: MedlinePlus

Maximum likelihood tree (partial sequences, 635 or 629 bp) showing the phylogenetic relationships of the amoA gene clone sequences obtained in this study to their closely related sequences from the GenBank database. One representative clone type within each OTU is shown, and the number of clones within each OTU is shown in parentheses. If there is only one clone sequence within a given OTU, the number “1” is omitted. The sequences from this study are bolded, and they are coded as follows for the example of XCDL-S-AOA-17: amoA sequences of clone no. 17 from the Xiaochaidan Lake sediment. Clone libraries QHL-14-W and QHL-14-S were corresponded to QLW1-0 and QLS-30 in Jiang et al. (2009b), respectively. The “R” symbol in some clone names denotes RNA-based (cDNA) clones. The underlined clone sequences were derived from the CrenamoA23f /CrenamoA616r primer set. The classification system of Pester et al. (2012) was employed. The letters “S” and “U” in the cluster names indicated “subcluster” and “unclassified.” The scale bars indicate the Jukes–Cantor distances. Bootstrap values of (1000 replicates) >50% are shown. The bacterial amoA gene from Nitrosococcus oceani was used as outgroup. Panels (A) and (B) are for waters and sediments, respectively.
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Figure 5: Maximum likelihood tree (partial sequences, 635 or 629 bp) showing the phylogenetic relationships of the amoA gene clone sequences obtained in this study to their closely related sequences from the GenBank database. One representative clone type within each OTU is shown, and the number of clones within each OTU is shown in parentheses. If there is only one clone sequence within a given OTU, the number “1” is omitted. The sequences from this study are bolded, and they are coded as follows for the example of XCDL-S-AOA-17: amoA sequences of clone no. 17 from the Xiaochaidan Lake sediment. Clone libraries QHL-14-W and QHL-14-S were corresponded to QLW1-0 and QLS-30 in Jiang et al. (2009b), respectively. The “R” symbol in some clone names denotes RNA-based (cDNA) clones. The underlined clone sequences were derived from the CrenamoA23f /CrenamoA616r primer set. The classification system of Pester et al. (2012) was employed. The letters “S” and “U” in the cluster names indicated “subcluster” and “unclassified.” The scale bars indicate the Jukes–Cantor distances. Bootstrap values of (1000 replicates) >50% are shown. The bacterial amoA gene from Nitrosococcus oceani was used as outgroup. Panels (A) and (B) are for waters and sediments, respectively.

Mentions: The amoA gene clone sequences obtained from the waters were grouped into the Nitrososphaera clusters (subcluster 1.1, 4.1, 8.1, 8.2, 10, and unclassified w1 and w2), Nitrosopumilus clusters and a “low salinity” cluster (Mosier and Francis, 2008; Figures 4B and 5A). The “low salinity” cluster was the predominant component (accounting for 62.6%) in the total water amoA gene clone sequences. The amoA gene clone sequences in the “low salinity” cluster had high an identity (~98%) with the clones from the San Francisco Bay estuary (Francis et al., 2005; Mosier and Francis, 2008) and a low-salinity ammonia-oxidizing archaeon “Candidatus Nitrosoarchaeum limnia” (Blainey et al., 2011). The amoA gene clone sequences in the Nitrosopumilus cluster were closely related (approximately 98% identity) to the clones retrieved from diverse environments, such as drinking water treatment plant (van der Wielen et al., 2009), Tibetan marsh wetland (unpublished), freshwater flow channel (Herrmann et al., 2011), waters near the Three Gorges Dam of Yangtze River (Huang et al., 2011), and freshwater sediment enrichment clones (AOA-AC5 and AOA-DW; French et al., 2012b). The amoA gene clone sequences in the Nitrososphaera cluster showed close relatedness (~98% identity) to clones from soils (unpublished), estuary sediments (Beman and Francis, 2006), Qinghai Lake sediments (Jiang et al., 2009b), and a AOA isolate Nitrososphaera viennensis EN76 (Tourna et al., 2011).


amoA-encoding archaea and thaumarchaeol in the lakes on the northeastern Qinghai-Tibetan Plateau, China.

Yang J, Jiang H, Dong H, Wang H, Wu G, Hou W, Liu W, Zhang C, Sun Y, Lai Z - Front Microbiol (2013)

Maximum likelihood tree (partial sequences, 635 or 629 bp) showing the phylogenetic relationships of the amoA gene clone sequences obtained in this study to their closely related sequences from the GenBank database. One representative clone type within each OTU is shown, and the number of clones within each OTU is shown in parentheses. If there is only one clone sequence within a given OTU, the number “1” is omitted. The sequences from this study are bolded, and they are coded as follows for the example of XCDL-S-AOA-17: amoA sequences of clone no. 17 from the Xiaochaidan Lake sediment. Clone libraries QHL-14-W and QHL-14-S were corresponded to QLW1-0 and QLS-30 in Jiang et al. (2009b), respectively. The “R” symbol in some clone names denotes RNA-based (cDNA) clones. The underlined clone sequences were derived from the CrenamoA23f /CrenamoA616r primer set. The classification system of Pester et al. (2012) was employed. The letters “S” and “U” in the cluster names indicated “subcluster” and “unclassified.” The scale bars indicate the Jukes–Cantor distances. Bootstrap values of (1000 replicates) >50% are shown. The bacterial amoA gene from Nitrosococcus oceani was used as outgroup. Panels (A) and (B) are for waters and sediments, respectively.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC3824093&req=5

Figure 5: Maximum likelihood tree (partial sequences, 635 or 629 bp) showing the phylogenetic relationships of the amoA gene clone sequences obtained in this study to their closely related sequences from the GenBank database. One representative clone type within each OTU is shown, and the number of clones within each OTU is shown in parentheses. If there is only one clone sequence within a given OTU, the number “1” is omitted. The sequences from this study are bolded, and they are coded as follows for the example of XCDL-S-AOA-17: amoA sequences of clone no. 17 from the Xiaochaidan Lake sediment. Clone libraries QHL-14-W and QHL-14-S were corresponded to QLW1-0 and QLS-30 in Jiang et al. (2009b), respectively. The “R” symbol in some clone names denotes RNA-based (cDNA) clones. The underlined clone sequences were derived from the CrenamoA23f /CrenamoA616r primer set. The classification system of Pester et al. (2012) was employed. The letters “S” and “U” in the cluster names indicated “subcluster” and “unclassified.” The scale bars indicate the Jukes–Cantor distances. Bootstrap values of (1000 replicates) >50% are shown. The bacterial amoA gene from Nitrosococcus oceani was used as outgroup. Panels (A) and (B) are for waters and sediments, respectively.
Mentions: The amoA gene clone sequences obtained from the waters were grouped into the Nitrososphaera clusters (subcluster 1.1, 4.1, 8.1, 8.2, 10, and unclassified w1 and w2), Nitrosopumilus clusters and a “low salinity” cluster (Mosier and Francis, 2008; Figures 4B and 5A). The “low salinity” cluster was the predominant component (accounting for 62.6%) in the total water amoA gene clone sequences. The amoA gene clone sequences in the “low salinity” cluster had high an identity (~98%) with the clones from the San Francisco Bay estuary (Francis et al., 2005; Mosier and Francis, 2008) and a low-salinity ammonia-oxidizing archaeon “Candidatus Nitrosoarchaeum limnia” (Blainey et al., 2011). The amoA gene clone sequences in the Nitrosopumilus cluster were closely related (approximately 98% identity) to the clones retrieved from diverse environments, such as drinking water treatment plant (van der Wielen et al., 2009), Tibetan marsh wetland (unpublished), freshwater flow channel (Herrmann et al., 2011), waters near the Three Gorges Dam of Yangtze River (Huang et al., 2011), and freshwater sediment enrichment clones (AOA-AC5 and AOA-DW; French et al., 2012b). The amoA gene clone sequences in the Nitrososphaera cluster showed close relatedness (~98% identity) to clones from soils (unpublished), estuary sediments (Beman and Francis, 2006), Qinghai Lake sediments (Jiang et al., 2009b), and a AOA isolate Nitrososphaera viennensis EN76 (Tourna et al., 2011).

Bottom Line: The results showed that the archaeal amoA gene was present in hypersaline lakes with salinity up to 160 g L(-) (1).Thaumarchaeol was present in all of the studied hypersaline lakes, even in those where no AEA amoA gene was observed.Future research is needed to determine the ecological function of AEA and possible sources of thaumarchaeol in the Qinghai-Tibetan hypersaline lakes.

View Article: PubMed Central - PubMed

Affiliation: State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences Wuhan, China ; Key Lab of Salt Lake Resources and Chemistry, Qinghai Institute of Salt Lakes, Chinese Academy of Sciences Xining, China.

ABSTRACT
All known ammonia-oxidizing archaea (AOA) belong to the phylum Thaumarchaeota within the domain Archaea. AOA possess the diagnostic amoA gene (encoding the alpha subunit of ammonia monooxygenase) and produce lipid biomarker thaumarchaeol. Although the abundance and diversity of amoA gene-encoding archaea (AEA) in freshwater lakes have been well-studied, little is known about AEA ecology in saline/hypersaline lakes. In this study, the distribution of the archaeal amoA gene and thaumarchaeol were investigated in nine Qinghai-Tibetan lakes with a salinity range from freshwater to salt-saturation (salinity: 325 g L(-) (1)). The results showed that the archaeal amoA gene was present in hypersaline lakes with salinity up to 160 g L(-) (1). The archaeal amoA gene diversity in Tibetan lakes was different from those in other lakes worldwide, suggesting Tibetan lakes (high elevation, strong ultraviolet, and dry climate) may host a unique AEA population of different evolutionary origin from those in other lakes. Thaumarchaeol was present in all of the studied hypersaline lakes, even in those where no AEA amoA gene was observed. Future research is needed to determine the ecological function of AEA and possible sources of thaumarchaeol in the Qinghai-Tibetan hypersaline lakes.

No MeSH data available.


Related in: MedlinePlus