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Bacterial diversity in snow on North Pole ice floes.

Hauptmann AL, Stibal M, Bælum J, Sicheritz-Pontén T, Brunak S, Bowman JS, Hansen LH, Jacobsen CS, Blom N - Extremophiles (2014)

Bottom Line: A total of 291,331 sequences were obtained through 454 pyrosequencing of 16S rRNA genes, resulting in 984 OTUs at 97 % identity.Principal component analysis showed that the three sites clustered together when compared to the underlying environments of sea ice and ocean water.The results support the idea that a globally distributed community exists in snow and that the global snow community can in part be attributed to microbial input from the atmosphere.

View Article: PubMed Central - PubMed

Affiliation: Center for Biosustainability, Technical University of Denmark, Hørsholm, Denmark.

ABSTRACT
The microbial abundance and diversity in snow on ice floes at three sites near the North Pole was assessed using quantitative PCR and 454 pyrosequencing. Abundance of 16S rRNA genes in the samples ranged between 43 and 248 gene copies per millilitre of melted snow. A total of 291,331 sequences were obtained through 454 pyrosequencing of 16S rRNA genes, resulting in 984 OTUs at 97 % identity. Two sites were dominated by Cyanobacteria (72 and 61 %, respectively), including chloroplasts. The third site differed by consisting of 95 % Proteobacteria. Principal component analysis showed that the three sites clustered together when compared to the underlying environments of sea ice and ocean water. The Shannon indices ranged from 2.226 to 3.758, and the Chao1 indices showed species richness between 293 and 353 for the three samples. The relatively low abundances and diversity found in the samples indicate a lower rate of microbial input to this snow habitat compared to snow in the proximity of terrestrial and anthropogenic sources of microorganisms. The differences in species composition and diversity between the sites show that apparently similar snow habitats contain a large variation in biodiversity, although the differences were smaller than the differences to the underlying environment. The results support the idea that a globally distributed community exists in snow and that the global snow community can in part be attributed to microbial input from the atmosphere.

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Principal component analysis (PCA) ordination of the microbial diversity data in the snow from the three North Pole sites. The first axis explains 31.8 % of the variation in the data, and the second axis explains 25.9 % of the variation in the data. The size of the circles is determined by the richness of the samples
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Fig2: Principal component analysis (PCA) ordination of the microbial diversity data in the snow from the three North Pole sites. The first axis explains 31.8 % of the variation in the data, and the second axis explains 25.9 % of the variation in the data. The size of the circles is determined by the richness of the samples

Mentions: The most abundant OTUs in sample A were chloroplasts (69.7 %), Burkholderiaceae (7 %) and Sphingomonas (4.5 %). Sample B was dominated by diatoms (Bacillariophyta, 30.9 %), (26.8 %), chloroplasts and Shewanella (11.6 %). The dominant OTUs in sample C were Pseudoalteromonas (26.8 %), Herbaspirillum (18.4 %) and Sphingomonas (7.9 %). The variation in diversity within samples (i.e., between replicates) was smaller than the variation between sites, which is visualised in a principal component analysis plot shown in Fig. 2, where replicates from the same site cluster together. This shows that errors potentially introduced during handling and analyses of the samples are smaller than the real differences between sites. At phylum level, the diversity of samples from site A and B was dominated by Cyanobacteria, including chloroplasts, (72 and 61 % respectively), Proteobacteria (23 and 35 %), Firmicutes (1.9 and 1.2 %) and Bacteroidetes (1.1 and 1.5 %) (Fig. 3). Sample C had similar abundances of Bacteroidetes (1.3 %) and Firmicutes (1.4 %) as in samples A and B, but was otherwise dominated by Proteobacteria (95 %) and lacked the high abundance of Cyanobacteria (1.4 %). Thus far most studies on snow have found Proteobacteria to be dominant, followed by Bacteroidetes and Actinobacteria (Bowers et al. 2009; Liu et al. 2009; Hell et al. 2013; Lopatina et al. 2013; Møller et al. 2013). Firmicutes have also shown to be common in snow (Bowers et al. 2009; Liu et al. 2009; Larose et al. 2010; Hell et al. 2013; Møller et al. 2013), as have Cyanobacteria (Bowers et al. 2009; Larose et al. 2010; Harding et al. 2011; Hell et al. 2013; Møller et al. 2013). The results of the present study are in line with previous findings that Proteobacteria, Bacteroidetes, Firmicutes and Cyanobacteria are the most abundant phyla in snow habitats. The similarity found between studies of snow from different locations supports the idea that a core community of bacteria might inhabit the snow habitat globally. Our study shows that the community composition at remote sites with minimum input from terrestrial and anthropogenic sources resembles that of sites in proximity to these sources and that the similarity in communities is, therefore, not a result of input from terrestrial ground, anthropogenic activities or as in our case the underlying environment of ice and ocean.Fig. 2


Bacterial diversity in snow on North Pole ice floes.

Hauptmann AL, Stibal M, Bælum J, Sicheritz-Pontén T, Brunak S, Bowman JS, Hansen LH, Jacobsen CS, Blom N - Extremophiles (2014)

Principal component analysis (PCA) ordination of the microbial diversity data in the snow from the three North Pole sites. The first axis explains 31.8 % of the variation in the data, and the second axis explains 25.9 % of the variation in the data. The size of the circles is determined by the richness of the samples
© Copyright Policy - OpenAccess
Related In: Results  -  Collection

Show All Figures
getmorefigures.php?uid=PMC4196135&req=5

Fig2: Principal component analysis (PCA) ordination of the microbial diversity data in the snow from the three North Pole sites. The first axis explains 31.8 % of the variation in the data, and the second axis explains 25.9 % of the variation in the data. The size of the circles is determined by the richness of the samples
Mentions: The most abundant OTUs in sample A were chloroplasts (69.7 %), Burkholderiaceae (7 %) and Sphingomonas (4.5 %). Sample B was dominated by diatoms (Bacillariophyta, 30.9 %), (26.8 %), chloroplasts and Shewanella (11.6 %). The dominant OTUs in sample C were Pseudoalteromonas (26.8 %), Herbaspirillum (18.4 %) and Sphingomonas (7.9 %). The variation in diversity within samples (i.e., between replicates) was smaller than the variation between sites, which is visualised in a principal component analysis plot shown in Fig. 2, where replicates from the same site cluster together. This shows that errors potentially introduced during handling and analyses of the samples are smaller than the real differences between sites. At phylum level, the diversity of samples from site A and B was dominated by Cyanobacteria, including chloroplasts, (72 and 61 % respectively), Proteobacteria (23 and 35 %), Firmicutes (1.9 and 1.2 %) and Bacteroidetes (1.1 and 1.5 %) (Fig. 3). Sample C had similar abundances of Bacteroidetes (1.3 %) and Firmicutes (1.4 %) as in samples A and B, but was otherwise dominated by Proteobacteria (95 %) and lacked the high abundance of Cyanobacteria (1.4 %). Thus far most studies on snow have found Proteobacteria to be dominant, followed by Bacteroidetes and Actinobacteria (Bowers et al. 2009; Liu et al. 2009; Hell et al. 2013; Lopatina et al. 2013; Møller et al. 2013). Firmicutes have also shown to be common in snow (Bowers et al. 2009; Liu et al. 2009; Larose et al. 2010; Hell et al. 2013; Møller et al. 2013), as have Cyanobacteria (Bowers et al. 2009; Larose et al. 2010; Harding et al. 2011; Hell et al. 2013; Møller et al. 2013). The results of the present study are in line with previous findings that Proteobacteria, Bacteroidetes, Firmicutes and Cyanobacteria are the most abundant phyla in snow habitats. The similarity found between studies of snow from different locations supports the idea that a core community of bacteria might inhabit the snow habitat globally. Our study shows that the community composition at remote sites with minimum input from terrestrial and anthropogenic sources resembles that of sites in proximity to these sources and that the similarity in communities is, therefore, not a result of input from terrestrial ground, anthropogenic activities or as in our case the underlying environment of ice and ocean.Fig. 2

Bottom Line: A total of 291,331 sequences were obtained through 454 pyrosequencing of 16S rRNA genes, resulting in 984 OTUs at 97 % identity.Principal component analysis showed that the three sites clustered together when compared to the underlying environments of sea ice and ocean water.The results support the idea that a globally distributed community exists in snow and that the global snow community can in part be attributed to microbial input from the atmosphere.

View Article: PubMed Central - PubMed

Affiliation: Center for Biosustainability, Technical University of Denmark, Hørsholm, Denmark.

ABSTRACT
The microbial abundance and diversity in snow on ice floes at three sites near the North Pole was assessed using quantitative PCR and 454 pyrosequencing. Abundance of 16S rRNA genes in the samples ranged between 43 and 248 gene copies per millilitre of melted snow. A total of 291,331 sequences were obtained through 454 pyrosequencing of 16S rRNA genes, resulting in 984 OTUs at 97 % identity. Two sites were dominated by Cyanobacteria (72 and 61 %, respectively), including chloroplasts. The third site differed by consisting of 95 % Proteobacteria. Principal component analysis showed that the three sites clustered together when compared to the underlying environments of sea ice and ocean water. The Shannon indices ranged from 2.226 to 3.758, and the Chao1 indices showed species richness between 293 and 353 for the three samples. The relatively low abundances and diversity found in the samples indicate a lower rate of microbial input to this snow habitat compared to snow in the proximity of terrestrial and anthropogenic sources of microorganisms. The differences in species composition and diversity between the sites show that apparently similar snow habitats contain a large variation in biodiversity, although the differences were smaller than the differences to the underlying environment. The results support the idea that a globally distributed community exists in snow and that the global snow community can in part be attributed to microbial input from the atmosphere.

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