Limits...
Ecology and Distribution of Thaumarchaea in the Deep Hypolimnion of Lake Maggiore.

Coci M, Odermatt N, Salcher MM, Pernthaler J, Corno G - Archaea (2015)

Bottom Line: In order to reach a high resolution at the Thaumarchaea community level, the probe MGI-535 was specifically designed for this study and applied to fluorescence in situ hybridization and catalyzed reporter deposition (CARD-FISH) analysis.We then applied it to a fine analysis of diversity and relative abundance of AOA in the deepest layers of the oligotrophic Lake Maggiore, confirming previous published results of AOA presence, but showing differences in abundance and distribution within the water column without significant seasonal trends with respect to Bacteria.Furthermore, phylogenetic analysis of AOA clone libraries from deep lake water and from a lake tributary, River Maggia, suggested the riverine origin of AOA of the deep hypolimnion of the lake.

View Article: PubMed Central - PubMed

Affiliation: Microbial Ecology Group, CNR-Institute of Ecosystem Study, Largo Tonolli 50, 28922 Verbania, Italy ; Microb&Co, Association for Microbial Ecology, Viale XX Settembre 45, 95128 Catania, Italy.

ABSTRACT
Ammonia-oxidizing Archaea (AOA) play an important role in the oxidation of ammonia in terrestrial, marine, and geothermal habitats, as confirmed by a number of studies specifically focused on those environments. Much less is known about the ecological role of AOA in freshwaters. In order to reach a high resolution at the Thaumarchaea community level, the probe MGI-535 was specifically designed for this study and applied to fluorescence in situ hybridization and catalyzed reporter deposition (CARD-FISH) analysis. We then applied it to a fine analysis of diversity and relative abundance of AOA in the deepest layers of the oligotrophic Lake Maggiore, confirming previous published results of AOA presence, but showing differences in abundance and distribution within the water column without significant seasonal trends with respect to Bacteria. Furthermore, phylogenetic analysis of AOA clone libraries from deep lake water and from a lake tributary, River Maggia, suggested the riverine origin of AOA of the deep hypolimnion of the lake.

Show MeSH
Bootstrapped maximum likelihood tree of sequenced 16S rRNA genes (GTR-GAMMA method, 1000 iterations). Blue colour indicates clones derived from River Maggia, while green and brown indicate clones from Lake Maggiore from spring (March) and autumn (September). Clusters in brown, green, and blue contain sequences from all three clone libraries. Numbers inside clusters refer to the number of sequences and OTUs, respectively. The bar at the bottom applies to 10% sequence divergence. The Nitrosopumilus (MGI) cluster contains sequences of N. maritimus (CP000866), “Ca. N. koreensis” (CP003842), and “Ca. N. salaria” (AEXL02000090); the cluster Nitrosoarchaeum contains sequences of “Ca. N. koreensis” (AFPU01000001) and “Ca. N. limnia” (AHJG01000224). The other two clusters include sequences of uncultured Archaea (reference sequences are HE589644 and KC437195 for SAGMGC-1 and AK31, resp.). For more details, see Figure S3 in Supplementary Material available online at http://dx.doi.org/10.1155/2015/590434.
© Copyright Policy - open-access
Related In: Results  -  Collection


getmorefigures.php?uid=PMC4561949&req=5

fig5: Bootstrapped maximum likelihood tree of sequenced 16S rRNA genes (GTR-GAMMA method, 1000 iterations). Blue colour indicates clones derived from River Maggia, while green and brown indicate clones from Lake Maggiore from spring (March) and autumn (September). Clusters in brown, green, and blue contain sequences from all three clone libraries. Numbers inside clusters refer to the number of sequences and OTUs, respectively. The bar at the bottom applies to 10% sequence divergence. The Nitrosopumilus (MGI) cluster contains sequences of N. maritimus (CP000866), “Ca. N. koreensis” (CP003842), and “Ca. N. salaria” (AEXL02000090); the cluster Nitrosoarchaeum contains sequences of “Ca. N. koreensis” (AFPU01000001) and “Ca. N. limnia” (AHJG01000224). The other two clusters include sequences of uncultured Archaea (reference sequences are HE589644 and KC437195 for SAGMGC-1 and AK31, resp.). For more details, see Figure S3 in Supplementary Material available online at http://dx.doi.org/10.1155/2015/590434.

Mentions: The 75 sequences were grouped in 8 OTUs on the base of ≥98% sequence similarity (Figure 5) and were all associated with Thaumarchaea. The River Maggia sample showed the highest diversity with 8 OTUs and a Shannon index of 0.75, whereas only two OTUs were recovered from Lake Maggiore samples and the diversity indices were 0.13 and 0.30 for spring and autumn, respectively. Rarefaction analyses suggest that the diversity of thaumarchaeal 16S rRNA genes was almost fully covered in Lake Maggiore clone libraries, whereas the River Maggia was still undersampled (Figure S4).


Ecology and Distribution of Thaumarchaea in the Deep Hypolimnion of Lake Maggiore.

Coci M, Odermatt N, Salcher MM, Pernthaler J, Corno G - Archaea (2015)

Bootstrapped maximum likelihood tree of sequenced 16S rRNA genes (GTR-GAMMA method, 1000 iterations). Blue colour indicates clones derived from River Maggia, while green and brown indicate clones from Lake Maggiore from spring (March) and autumn (September). Clusters in brown, green, and blue contain sequences from all three clone libraries. Numbers inside clusters refer to the number of sequences and OTUs, respectively. The bar at the bottom applies to 10% sequence divergence. The Nitrosopumilus (MGI) cluster contains sequences of N. maritimus (CP000866), “Ca. N. koreensis” (CP003842), and “Ca. N. salaria” (AEXL02000090); the cluster Nitrosoarchaeum contains sequences of “Ca. N. koreensis” (AFPU01000001) and “Ca. N. limnia” (AHJG01000224). The other two clusters include sequences of uncultured Archaea (reference sequences are HE589644 and KC437195 for SAGMGC-1 and AK31, resp.). For more details, see Figure S3 in Supplementary Material available online at http://dx.doi.org/10.1155/2015/590434.
© Copyright Policy - open-access
Related In: Results  -  Collection

Show All Figures
getmorefigures.php?uid=PMC4561949&req=5

fig5: Bootstrapped maximum likelihood tree of sequenced 16S rRNA genes (GTR-GAMMA method, 1000 iterations). Blue colour indicates clones derived from River Maggia, while green and brown indicate clones from Lake Maggiore from spring (March) and autumn (September). Clusters in brown, green, and blue contain sequences from all three clone libraries. Numbers inside clusters refer to the number of sequences and OTUs, respectively. The bar at the bottom applies to 10% sequence divergence. The Nitrosopumilus (MGI) cluster contains sequences of N. maritimus (CP000866), “Ca. N. koreensis” (CP003842), and “Ca. N. salaria” (AEXL02000090); the cluster Nitrosoarchaeum contains sequences of “Ca. N. koreensis” (AFPU01000001) and “Ca. N. limnia” (AHJG01000224). The other two clusters include sequences of uncultured Archaea (reference sequences are HE589644 and KC437195 for SAGMGC-1 and AK31, resp.). For more details, see Figure S3 in Supplementary Material available online at http://dx.doi.org/10.1155/2015/590434.
Mentions: The 75 sequences were grouped in 8 OTUs on the base of ≥98% sequence similarity (Figure 5) and were all associated with Thaumarchaea. The River Maggia sample showed the highest diversity with 8 OTUs and a Shannon index of 0.75, whereas only two OTUs were recovered from Lake Maggiore samples and the diversity indices were 0.13 and 0.30 for spring and autumn, respectively. Rarefaction analyses suggest that the diversity of thaumarchaeal 16S rRNA genes was almost fully covered in Lake Maggiore clone libraries, whereas the River Maggia was still undersampled (Figure S4).

Bottom Line: In order to reach a high resolution at the Thaumarchaea community level, the probe MGI-535 was specifically designed for this study and applied to fluorescence in situ hybridization and catalyzed reporter deposition (CARD-FISH) analysis.We then applied it to a fine analysis of diversity and relative abundance of AOA in the deepest layers of the oligotrophic Lake Maggiore, confirming previous published results of AOA presence, but showing differences in abundance and distribution within the water column without significant seasonal trends with respect to Bacteria.Furthermore, phylogenetic analysis of AOA clone libraries from deep lake water and from a lake tributary, River Maggia, suggested the riverine origin of AOA of the deep hypolimnion of the lake.

View Article: PubMed Central - PubMed

Affiliation: Microbial Ecology Group, CNR-Institute of Ecosystem Study, Largo Tonolli 50, 28922 Verbania, Italy ; Microb&Co, Association for Microbial Ecology, Viale XX Settembre 45, 95128 Catania, Italy.

ABSTRACT
Ammonia-oxidizing Archaea (AOA) play an important role in the oxidation of ammonia in terrestrial, marine, and geothermal habitats, as confirmed by a number of studies specifically focused on those environments. Much less is known about the ecological role of AOA in freshwaters. In order to reach a high resolution at the Thaumarchaea community level, the probe MGI-535 was specifically designed for this study and applied to fluorescence in situ hybridization and catalyzed reporter deposition (CARD-FISH) analysis. We then applied it to a fine analysis of diversity and relative abundance of AOA in the deepest layers of the oligotrophic Lake Maggiore, confirming previous published results of AOA presence, but showing differences in abundance and distribution within the water column without significant seasonal trends with respect to Bacteria. Furthermore, phylogenetic analysis of AOA clone libraries from deep lake water and from a lake tributary, River Maggia, suggested the riverine origin of AOA of the deep hypolimnion of the lake.

Show MeSH