Abundance, viability and diversity of the indigenous microbial populations at different depths of the NEEM Greenland ice core

Figures & data

Table 1 Characteristics of decontaminated North Greenland Eemian Ice Drilling core samples subjected to microbiological analyses.

Sample depth from top (m) and bag number	Core length	Ice age (years b2k)^a	Ice type	Ca^2 + (ng/g)	Dust (#/mL) (>1.0 mm)	Cell abundance (cells/ml) (mean±SD)	Viability live/dead staining (%)	Isolates (CFU/ml)	Culturability CFU^b/ml cell counts/ml (%)
101.2 100d	20 cm	355	Bubbly	NA	NA	2.53×10^6±1.52	83.8	2.25	0.000089
633.05 bag 1152	55 cm	3232	Brittle	NA	NA	1.33×10^5±1.01	77.9	10.25	0.0077
643.5 bag 1172	50 cm	3298	Brittle	NA	NA	9.47×10^4±3.8	56.7	15.75	0.0166
1729.75 bag 3146	15 cm	36 200	Clathrated	283.938	91 968	3.67×10^6±1.3	39.1	12.25	0.00033
2051.5 bag 3731	30 cm	80 382	Clathrated	43.401	6809	3.59×10^5±1.0	84.5	1.0	0.00028

^aAges of the studied samples were derived from Rasmussen et al. (2013) and NEEM Community Members (2013). B2k stands for years before 2000. ^bColony-forming units.

Fig. 1 Distribution of colony-forming units (CFU) representing different phyla/classes cultivated from each North Greenland Eemian Ice Drilling core sample.

Fig. 2 Phylogenetic relationships of small subunit rRNA genes of isolates from decontaminated North Greenland Eemian Ice Drilling core samples from different depths. The tree is based on distance analysis (neighbour-joining algorithm with the Juke-Cantor model). Bootstrap values greater than 50% generated from 100 replicates are shown above the nodes. Accession numbers for these isolates and for closely related environmental cultured representatives retrieved from databases are included. Area in grey highlights the subcluster of the novel alphaproteobacterium and its closest relatives.

Table 2 Number of isolate small subunit rRNA gene sequences observed operational taxonomic units (S_obs), richness and diversity indices for North Greenland Eemian Ice Drilling core samples from different depths.

Label	Sample depth (m)	Number of sequences	Sobs	Chao1	Shannon	Inverse Simpson
V1	101.20	4	4	10	1.39	1.00
V2	1729.75	19	7	8	1.67	5.34
V3	2051.50	4	4	10	1.39	1.00
V4	633.05/643.5	14	7	12	1.57	4.13

Fig. 3 Neighbour-joining tree of SSU rRNA gene clone sequences from different depths of North Greenland Eemian Ice Drilling glacial ice. For groups with highly similar clone sequences from the same ice core sample, a single representative was chosen. Bootstrap values greater than 50% generated from 1000 replicates are shown above the nodes.

Table 3 Number of small subunit rRNA gene clone sequences, observed operational taxonomic units (S_obs), richness and diversity indices at genus level for North Greenland Eemian Ice Drilling core samples from different depths.

Label	Sample depth (m)	Number of sequences	Sobs	Chao1	Shannon	Inverse Simpson
V1	101.20	22	4	4	0.98	2.26
V2	1729.75	28	5	6	1.19	2.91
V3	2051.50	41	5	5.5	0.67	1.45
V4	633.05/643.5	65	4	4	0.77	1.73

Table 4 Number of Illumina small subunit rRNA gene sequences, observed operational taxonomic units (S_obs), richness and diversity indices for North Greenland Eemian Ice Drilling core samples from different depths. The average values (±SD) were calculated for genus level. A normalized equal number of sequences (341 215) from each sample were randomly selected for analysis.

Label	Sample depth (m)	Number of sequences	Sobs	Chao1	Shannon	Inverse Simpson
V1	101.20	341 215	446 (±0)	675 (±0)	0.58 (±0)	1.35 (±0)
V2	1729.75	861 394	296 (±7.3)	459 (±39)	0.93 (±0.0014)	2.12 (±0.0017)
V3	2051.50	957 514	336 (±8.9)	539 (±46)	0.88 (±0.0021)	1.54 (±0.0019)
V4	633.05	991 957	118 (±4.8)	188 (±29)	0.53 (±0.0017)	1.29 (±0.0012)

Fig. 4 Rarefaction curves of phylotype based operational taxonomic units (OTUs) of the small subunit rRNA gene Illumina sequence reads for North Greenland Eemian Ice Drilling core samples from different depths. Phylotype levels include genus (triangles), family (dots) and order (rectangles).

Fig. 5 Distribution of major phyla/classes of small subunit rRNA gene sequences generated by Illumina MiSeq sequencing. The number of reads for each column is given in parentheses. Groups are shown in numerically descending order of sequence reads.

Fig. 6 Relative abundance of genera in North Greenland Eemian Ice Drilling core samples from different depths based on Illumina MiSeq sequencing. Left panels show the most abundant genera (>1%). Right panels show less frequently detected genera (0.02–1%).

Fig. 7 Principle coordinate analysis of operational taxonomic unit abundance in all samples. Plots of beta diversity were calculated based on weighted Unifrac metrics. The percent variations explained by each coordinate are shown on each axis.

Fig. 8 Distribution of dominant phylogenetic groups in populations from different North Greenland Eemian Ice Drilling ice depths revealed by: (a) cultivation/direct plating; (b) Sanger clone libraries; (c) Illumina next-generation sequencing. Column graphs show percentage of small subunit rRNA gene sequences assigned to different phyla/classes. Dendrograms represent the population structure similarity between the samples at class level based on the thetayc coefficient.

Rasmussen S.O., Abbott P., Blunier T., Bourne A., Brook E., Buchardt S.L., Buizert C., Chappellaz J., Clausen H.B., Cook E., Davies S., Guillevic M., Kipfstuhl S., Laepple T., Dahl-Jensen D., Seierstad I.K., Severinghaus J.P., Steffensen J.P., Stowasser C., Svensson A., Vallelonga P., Vinther B.M., Wilhelms F., Winstrup M. A first chronology for the NEEM ice core. Climate Past Discussions. 2013; 9: 2967–3013.

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