Table 4

Summaries of the four environmental microbial community datasets
Dataset summary Resulting data
Acid mine drainage bacteria and archaea Total RNA was collected from 8 environmental biofilms and 5 bioreactor biofilms at varying stages of development: early (GS0), mid (GS1), and late (GS2). RNA from all samples was converted to cDNA. 6 environmental and 2 bioreactor samples were sequenced using HiSeq 2500 Illumina. 2 environmental and 3 bioreactor samples were sequenced using GAIIx Illumina. 159 SSU-rRNA sequence fragments were identified in 13 biofilms. The number of reads and SSU-rRNA sequences assembled from the GAIIx and the HiSeq platforms differed greatly; thus the rarefied data from these sequencing methods were analyzed separately (HiSeq: Figure 2, GAIIx: Additional file 1: Figure S1).
Hypersaline lake viruses 8 surface water samples were collected within a hypersaline lake as follows: Jan. 2007 (2 samples, site A, 2 days apart, 2007At1, 2007At2), Jan. 2009 (1 sample, site B, 2009B), Jan. 2010 (1 sample, site A, 2010A; 4 samples, site B, each ~1 day apart, 2010Bt1, 2010Bt2, 2010Bt3, 2010Bt4). 454-Titanium was used to sequence samples 2010Bt1 and 2010Bt3. Illumina GAIIx was used to sequence the remaining 6 samples. 630 methyltransferase genes, 411 concanavalin A-like glucanases/lectins, and 71 putative genes falling under Cluster 667 were assembled from the viral metagenomic reads (Methyltransferase: Additional file 1: Figure S2, Concanavalin: Additional file 1: Figure S3, Cluster 667: Figure 1).
Subsurface bacteria DNA was extracted from 5 sediment samples taken from in situ flow-through columns buried in sampling wells in a shallow, uranium and vanadium-contaminated aquifer: background sediment (B), sediment stimulated with carbon and vanadium addition (V1, V2), and sediment stimulated with carbon addition alone (A1, A2). HiSeq Illumina was used to sequence 16S SSU-rRNA PCR product. 25,966 OTUs were identified from 5 subsurface samples (Figure 3).
Substrate-associated soil fungi DNA was extracted from 32 straw bait bags and 32 wood blocks that were buried in grassland and forest (16 straw and 16 wood in each). Half of the substrates were buried for six months (time point 1) and half for 18 months (time point 2). 454-Titanium was used to sequence the PCR amplified LSU region. 508 total OTUs were identified within all substrate samples (Grassland: Figure 4, Forest: Additional file 1: Figure S4).

Doll et al.

Doll et al. BMC Microbiology 2013 13:259   doi:10.1186/1471-2180-13-259

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