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. 2011 Mar 31;6(3):e18320. doi: 10.1371/journal.pone.0018320

Table 1. Summary of nutrient-induced shifts in relative abudance of dominant bacterial lineages.

Represent. Clone Amplicon In silico LIGHT DARK Relevant
Phylum Concensus clade1 Accession count2 TRF (bp)3 TRF(bp)3 N P N P Figure
Actinobacteria Microbacteriaceae EU914094 8 228.23 230 − −* 5b
Actinobacteria Actinomycetales EU914093 18 223.42 227 −* +* − 5a,6a
Actinobacteria Sporichthyaceae EU914097 20 221.92 225
Bacteriodetes Flavobacteriaceae EU914089 25 518.02 515–5174 +* 6d
Bacteriodetes Chitinophagaceae EU914013 14 326.16 327 +* 6e
Bacteriodetes Sphingobacteriales EU914014 27 31.38 39
β-proteobacteria Alcaligenaceae EU914084 6 216.28 219 +
β-proteobacteria Polaromonads EU914062 9 317.44 319 0 0 5e
β-proteobacteria Comamonadaceae EU914088 6 212.21 215 − 5c
β-proteobacteria Comamonadaceae EU914006 15 217.90 217 −* 6c
β-proteobacteria Burkholderiales EU914083 12 196.28 200 0 0 +* 5d
Cyanobacteria Subsection I EU914078 5 220.41 224 −* 0 0 6b
Verrucomicrobia Opitutaceae EU914072 7 218.37 222 +

Symbols are as follows: +  =  increased relative contribution during experiment, −  =  decreased relative contribution during experiment, * = p<0.05, no star  = p<0.1, blank  = p>0.1, 0 =  absent from treatment. Temporal dynamics of treatment responses are detailed in Figs. 5 and 6.

1

Clades are concensus classified to the most reduced taxonomic level where all clone sequences with the same in silico TRF length are classified with >95% probability by Bayesian classifier with the curated SILVA 16S sequence alignment. Clades are defined based on monophyletic in silico and measured TRF lengths of clones using the tree in Fig. S1.

2

Counts are the number of clones sequenced from Emerald Lake that satisy criteria of both having matching in silico TRF lengths across four clone libraries (96 clones each) reported in Nelson (2009) and sharing concensus classification within the SILVA 16S database. Clones and respective classifications are listed in Table S2. Clones are placed in phylogenetic context in a tree in Fig. S1.

3

TRF lengths are from amplicon digestions based on running cloned 16S DNA through TRFLP (left column) and in silico digestions based on the location of the restriction site in sequences (right column) of representative clones using the enzyme Hae III. Note that it is common to find discrepancies between predicted and actual TRF lengths; for further details see Nelson (2009).

4

Although the Flavobacteriaceae are split into two distinct clades with monophyletic in silico TRF lengths these clades could not be differentiated on actual TRFLP fragment analyses: representative clones from both clades ran at ∼518 bp.