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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.

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Bubble chart showing relative DGGE band intensities of lake water samples at 50, 200, and 350 m depth (Ghiffa pelagic station) and River Maggia in April, June, and August 2011. 16S rRNA and amoA gene patterns are displayed both for Bacteria and Archaea. X denotes absence of amplified bands. The primer sets applied are different between different amplifications, and the comparison between intensities should be considered only within the same set (vertical columns).
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fig4: Bubble chart showing relative DGGE band intensities of lake water samples at 50, 200, and 350 m depth (Ghiffa pelagic station) and River Maggia in April, June, and August 2011. 16S rRNA and amoA gene patterns are displayed both for Bacteria and Archaea. X denotes absence of amplified bands. The primer sets applied are different between different amplifications, and the comparison between intensities should be considered only within the same set (vertical columns).

Mentions: The spatial distribution of ammonia-oxidizing prokaryotes assessed by PCR-DGGE was different for Bacteria and Archaea. Ammonia-oxidizing Bacteria (AOB) were detected at 50, 200, and 350 m depth in the lake but not in River Maggia (Figure 4). No PCR inhibitors were present in river sample based on positive amplification of lake and river DNA mixture. DGGE profiles of the AOB-16S rRNA obtained with CTO-primer set in July consisted of 4 bands and were identical for all depths with a significant decrease in signal intensities from 50 m to 350 m depth. Same pattern of band signal decrease was observed for bacterial amoA gene profile in April and June, which consisted of 5 bands. AOA, in contrast, were detected both in the lake and in the river samples except for April when no AOA were detected in the river. The archaeal 16S rRNA DGGE profiles consisted of 4 bands and were identical at all depths in the lake and also in the river samples. The archaeal amoA DGGE profiles assessed in April and June consisted of 3 bands. Bands from archaeal 16S rRNA and amoA profiles were excised, reamplified, and separated on denaturing gels till obtaining pure bands for sequencing. The procedure revealed that only one major band of 16S rRNA gene was present in all samples, the other bands being heteroduplexes [43]; sequence LM_50 m_band1 (232 bp) was deposited to GenBank as example (XXXXXXXX). Based on BLAST analysis, sequences obtained from samples at 50-200-350 m depth and River Maggia showed between 98 and 100% identity with the partial 16S rRNA gene sequences of the uncultured Thaumarchaeota clone VWS114 detected by Vissers et al. [15] in Lake Lucerne. Excision and reamplification of bands from AOA_amoA gel profile revealed also that only one major band was present, the others being heteroduplexes; sequence LM_200 m_band5 was deposited to GenBank as example (accession number XXXXXXXX); BLAST analysis showed 99% identity with isolated DGGE gel bands of uncultured crenarchaeon from marine environment and isolated clones from estuarine environments.


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

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

Bubble chart showing relative DGGE band intensities of lake water samples at 50, 200, and 350 m depth (Ghiffa pelagic station) and River Maggia in April, June, and August 2011. 16S rRNA and amoA gene patterns are displayed both for Bacteria and Archaea. X denotes absence of amplified bands. The primer sets applied are different between different amplifications, and the comparison between intensities should be considered only within the same set (vertical columns).
© Copyright Policy - open-access
Related In: Results  -  Collection

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getmorefigures.php?uid=PMC4561949&req=5

fig4: Bubble chart showing relative DGGE band intensities of lake water samples at 50, 200, and 350 m depth (Ghiffa pelagic station) and River Maggia in April, June, and August 2011. 16S rRNA and amoA gene patterns are displayed both for Bacteria and Archaea. X denotes absence of amplified bands. The primer sets applied are different between different amplifications, and the comparison between intensities should be considered only within the same set (vertical columns).
Mentions: The spatial distribution of ammonia-oxidizing prokaryotes assessed by PCR-DGGE was different for Bacteria and Archaea. Ammonia-oxidizing Bacteria (AOB) were detected at 50, 200, and 350 m depth in the lake but not in River Maggia (Figure 4). No PCR inhibitors were present in river sample based on positive amplification of lake and river DNA mixture. DGGE profiles of the AOB-16S rRNA obtained with CTO-primer set in July consisted of 4 bands and were identical for all depths with a significant decrease in signal intensities from 50 m to 350 m depth. Same pattern of band signal decrease was observed for bacterial amoA gene profile in April and June, which consisted of 5 bands. AOA, in contrast, were detected both in the lake and in the river samples except for April when no AOA were detected in the river. The archaeal 16S rRNA DGGE profiles consisted of 4 bands and were identical at all depths in the lake and also in the river samples. The archaeal amoA DGGE profiles assessed in April and June consisted of 3 bands. Bands from archaeal 16S rRNA and amoA profiles were excised, reamplified, and separated on denaturing gels till obtaining pure bands for sequencing. The procedure revealed that only one major band of 16S rRNA gene was present in all samples, the other bands being heteroduplexes [43]; sequence LM_50 m_band1 (232 bp) was deposited to GenBank as example (XXXXXXXX). Based on BLAST analysis, sequences obtained from samples at 50-200-350 m depth and River Maggia showed between 98 and 100% identity with the partial 16S rRNA gene sequences of the uncultured Thaumarchaeota clone VWS114 detected by Vissers et al. [15] in Lake Lucerne. Excision and reamplification of bands from AOA_amoA gel profile revealed also that only one major band was present, the others being heteroduplexes; sequence LM_200 m_band5 was deposited to GenBank as example (accession number XXXXXXXX); BLAST analysis showed 99% identity with isolated DGGE gel bands of uncultured crenarchaeon from marine environment and isolated clones from estuarine environments.

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
Related in: MedlinePlus