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
Relative proportions (±s.d.) of hybridized cells in Lake Maggiore in 2011 (Ghiffa sampling station) for Bacteria (probe EUB I–III), Archaea (probe ARC915), and Thaumarchaea of the Marine Group I (probe MGI-535) at 200 m (a) and 350 m (b). Boxplot of hybridization rates (c) for the same samples (Ghiffa station, 2011). Whiskers indicate Tukey's 1.5 IQR. Significant differences in mean between 200 m and 350 m were detected for ARC915 (p < 0.01) and EUB I–III (p = 0.05).
© Copyright Policy - open-access
Related In: Results  -  Collection


getmorefigures.php?uid=PMC4561949&req=5

fig3: Relative proportions (±s.d.) of hybridized cells in Lake Maggiore in 2011 (Ghiffa sampling station) for Bacteria (probe EUB I–III), Archaea (probe ARC915), and Thaumarchaea of the Marine Group I (probe MGI-535) at 200 m (a) and 350 m (b). Boxplot of hybridization rates (c) for the same samples (Ghiffa station, 2011). Whiskers indicate Tukey's 1.5 IQR. Significant differences in mean between 200 m and 350 m were detected for ARC915 (p < 0.01) and EUB I–III (p = 0.05).

Mentions: Total hybridization rates (sum of probes ARC915 and EUB I–III) ranged between 60 and 99% of DAPI stained cells except for two outliers (June 8, 109.1%; July 13, 104.5%). The proportion of hybridized Bacteria (probe EUB I–III) ranged from 40.9% to 58.2% of total DAPI stained cells (mean: 49.1 ± 4.3%, Figure 3) at 200 m and from 42.3% to 64.3% (mean: 52.3 ± 5.8%) at 350 m. Relative abundance of Archaea (probe ARC915) ranged from 14.7% to 31.3% (mean: 25.3 ± 5.8%) at 200 m and from 19.6% to 49.4% (mean: 33.4 ± 10.0%) at 350 m depth. The newly designed probe MGI-535 targets 2108 almost full-length sequences affiliated with MGI-Thaumarchaea (91.1% clade coverage). By allowing one mismatch, this probe theoretically detects 68 additional sequences affiliated with the SAGMCG-1 clade; however, all false-positive hits have a strong central mismatch. Thus, this probe is very specific for MGI-Thaumarchaea. Relative abundance of MGI-Thaumarchaea ranged from 9.2% to 13.1% (mean: 10.9 ± 1.2%) at 200 m and from 8.5% to 14.1% (mean: 11.5 ± 1.2%) at 350 m. All three groups showed no significant variation in relative proportions throughout the sampling period, neither at 200 m nor at 350 m depth (Figure 3). The two depths significantly differed for ARC915 (p < 0.01) and EUB I–III (p = 0.05), while no significant difference was detected for MGI-535 (Wilcoxon rank sum test). Seasonal variability (coefficient of variation, CV) was higher for ARC915 (22.88% at 200 m, 29.9% at 350 m) than for EUB I–III (8.7% at 200 m, 11.2% at 350 m) and MGI-Thaumarchaea (10.8% at 200 m, 15.6% at 350 m) where sampling variability was within the range of the overall variability (Figure S2). Hybridization rates of MGI-Thaumarchaea were tested by ANOVA to confirm the presence of true difference between the samples (p = 0.014 at 200 m, p < 0.01 at 350 m) and a Tukey HSD post hoc test revealed that differences between samples were higher at 350 m than at 200 m depth. Total numbers of MGI-Thaumarchaea were 7.6 × 104  ± 2.5 × 104 cells mL−1 at 200 m and 7.3 × 104  ± 1.9 × 104 cells mL−1 at 350 m depth. There was no significant difference between the two depths and there were no significant intra-annual variations.


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

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

Relative proportions (±s.d.) of hybridized cells in Lake Maggiore in 2011 (Ghiffa sampling station) for Bacteria (probe EUB I–III), Archaea (probe ARC915), and Thaumarchaea of the Marine Group I (probe MGI-535) at 200 m (a) and 350 m (b). Boxplot of hybridization rates (c) for the same samples (Ghiffa station, 2011). Whiskers indicate Tukey's 1.5 IQR. Significant differences in mean between 200 m and 350 m were detected for ARC915 (p < 0.01) and EUB I–III (p = 0.05).
© Copyright Policy - open-access
Related In: Results  -  Collection

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

fig3: Relative proportions (±s.d.) of hybridized cells in Lake Maggiore in 2011 (Ghiffa sampling station) for Bacteria (probe EUB I–III), Archaea (probe ARC915), and Thaumarchaea of the Marine Group I (probe MGI-535) at 200 m (a) and 350 m (b). Boxplot of hybridization rates (c) for the same samples (Ghiffa station, 2011). Whiskers indicate Tukey's 1.5 IQR. Significant differences in mean between 200 m and 350 m were detected for ARC915 (p < 0.01) and EUB I–III (p = 0.05).
Mentions: Total hybridization rates (sum of probes ARC915 and EUB I–III) ranged between 60 and 99% of DAPI stained cells except for two outliers (June 8, 109.1%; July 13, 104.5%). The proportion of hybridized Bacteria (probe EUB I–III) ranged from 40.9% to 58.2% of total DAPI stained cells (mean: 49.1 ± 4.3%, Figure 3) at 200 m and from 42.3% to 64.3% (mean: 52.3 ± 5.8%) at 350 m. Relative abundance of Archaea (probe ARC915) ranged from 14.7% to 31.3% (mean: 25.3 ± 5.8%) at 200 m and from 19.6% to 49.4% (mean: 33.4 ± 10.0%) at 350 m depth. The newly designed probe MGI-535 targets 2108 almost full-length sequences affiliated with MGI-Thaumarchaea (91.1% clade coverage). By allowing one mismatch, this probe theoretically detects 68 additional sequences affiliated with the SAGMCG-1 clade; however, all false-positive hits have a strong central mismatch. Thus, this probe is very specific for MGI-Thaumarchaea. Relative abundance of MGI-Thaumarchaea ranged from 9.2% to 13.1% (mean: 10.9 ± 1.2%) at 200 m and from 8.5% to 14.1% (mean: 11.5 ± 1.2%) at 350 m. All three groups showed no significant variation in relative proportions throughout the sampling period, neither at 200 m nor at 350 m depth (Figure 3). The two depths significantly differed for ARC915 (p < 0.01) and EUB I–III (p = 0.05), while no significant difference was detected for MGI-535 (Wilcoxon rank sum test). Seasonal variability (coefficient of variation, CV) was higher for ARC915 (22.88% at 200 m, 29.9% at 350 m) than for EUB I–III (8.7% at 200 m, 11.2% at 350 m) and MGI-Thaumarchaea (10.8% at 200 m, 15.6% at 350 m) where sampling variability was within the range of the overall variability (Figure S2). Hybridization rates of MGI-Thaumarchaea were tested by ANOVA to confirm the presence of true difference between the samples (p = 0.014 at 200 m, p < 0.01 at 350 m) and a Tukey HSD post hoc test revealed that differences between samples were higher at 350 m than at 200 m depth. Total numbers of MGI-Thaumarchaea were 7.6 × 104  ± 2.5 × 104 cells mL−1 at 200 m and 7.3 × 104  ± 1.9 × 104 cells mL−1 at 350 m depth. There was no significant difference between the two depths and there were no significant intra-annual variations.

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