Table 2. Relative abundance and phylogenetic affiliation of sequenced phylotypes.
| 2006 | 2008 | ||||||||||||||||||||
| 0.22–8 μm | >8 μm | 0.22–5 μm | >5 μm | ||||||||||||||||||
| OTUs | C-L | RB0.05-L | RB0.2-L | HP10-L | C-L | RB0.05-L | RB0.2-L | HP10-L | C-L | RB0.02-L | HP10-L | C-L | RB0.02-L | HP10-L | Freshwatercluster | RDP Naive Bayesian rRNAClassifier | BLAST results | ||||
| β-Proteobacteria | 1 | 31 | 17 | 4 | 9 | 2 | 2 | 4 | 13 | 30 | 8 | 4 | 2 | bet II, PnecC | Burkholderiaceae | 100% | 99% | P. necessariusQLW-P1-DMWA-1T | CP000655 | ||
| 2 | 4 | 2 | 6 | bet II, PnecA | Burkholderiaceae | 100% | 97% | P. acidophobusMWH-PoolGreenA3 | FM208180 | ||||||||||||
| 3 | 2 | 2 | 13 | 2 | 13 | 20 | 4 | 2 | 2 | bet I, Lhab-A4 | Comamonadaceae | 98% | 99% | Lake GrosseFuchskuhle clone FNE11-10 | DQ501302 | ||||||
| 4 | 19 | 2 | 2 | 2 | 2 | 2 | bet IV, RDP18A09 | Methylophilaceae | 100% | 98% | Parker river clonePRD18A09 | AY947994 | |||||||||
| 5 | 4 | bet III, betIII-A1 | Alcaligenaceae | 100% | 99% | Grosse Lacke isolateQLW-p2DMWB-4 | AJ938031 | ||||||||||||||
| 6 | 2 | 4 | 2 | 4 | bet I, Lhab-A4 | Comamonadaceae | 100% | 97% | Lake IJssel clone Stal-17 | AJ416187 | |||||||||||
| 7 | 4 | 6 | 4 | 6 | bet VII | Oxalobacteraceae | 100% | 97% | Lake Grosse Fuchskuhleclone NE45 | AJ575695 | |||||||||||
| α-Proteobacteria | 8 | 9 | 36 | 2 | 4 | 7 | 4 | 2 | 16 | 6 | 13 | alf IV-A, Novo-A1 | Sphingomonadaceae | 100% | 99% | N. acidiphilumFSW06-204dT | EU336977 | ||||
| 9 | 19 | 11 | 2 | Bradyrhizobiaceae | 15% | 96% | Lake Pohlseeclone Hv_38 | EF667926 | |||||||||||||
| 10 | 7 | Hyphomicrobiaceae | 36% | 90% | Mesorhizobium sp.CCBAU 33182 | GU433452 | |||||||||||||||
| 11 | 2 | 4 | 9 | 2 | alf II | Caulobacteraceae | 100% | 97% | Adriondack lake cloneADK-BTe02-51 | EF520395 | |||||||||||
| 12 | 4 | Hyphomicrobiaceae | 46% | 98% | Rhodomicrobium vannieliiE.Y. 33T | M34127 | |||||||||||||||
| 13 | 7 | 2 | alf I, alf I-B1 | Beijerinckiaceae | 69% | 98% | Lake Grosse Fuchskuhleisolate FSW06-301 | FJ798303 | |||||||||||||
| 14 | 2 | 9 | alf VIII | Acetobacteraceae | 100% | 95% | Asaia lannaensis BCC 15733T | AB286050 | |||||||||||||
| γ-Proteobacteria | 15 | 2 | 58 | 2 | 13 | close to gam III | Methylococcaceae | 100% | 95% | Hypertrophic freshwater lakeclone ML-9-70.2 | DQ520192 | ||||||||||
| 16 | 7 | 7 | 15 | Legionellaceae | 100% | 96% | Legionella longbeachaeATCC 33484 | AY444741 | |||||||||||||
| 17 | 4 | 4 | 6 | Legionellaceae | 99% | 92% | Legionella impletisoliOA1-1T | AB233209 | |||||||||||||
| 18 | 4 | Ectothiorhodospiraceae | 70% | 96% | Activated sludge cloneAS1o9 | AJ514448 | |||||||||||||||
| 19 | 2 | 6 | 19 | 4 | gam I | Methylococcaceae | 100% | 96% | Methylomonas rubraNCIMB 11913 | AF304194 | |||||||||||
| Actinobacteria | 20 | 15 | 33 | 4 | 2 | 23 | 16 | 2 | acI-B, scB-3 | Microbacteriaceae | 45% | 99% | Lake Grosse Fuchskuhleclone FSW11-16 | DQ316348 | |||||||
| Firmicutes | 21 | 2 | 4 | 2 | 17 | 27 | 8 | Paenibacillaceae | 95% | 93% | Paenibacillus polymyxa SC2 | CP002213 | |||||||||
| Chlorobii | 22 | 4 | 2 | 2 | 9 | 17 | 17 | Chlorobiaceae | 100% | 98% | Pelodictyon phaeoclathratiformeBU-1T | CP001110 | |||||||||
| Bacteroidetes | 23 | 2 | 11 | 4 | 4 | 13 | 4 | Chitinophagaceae | 100% | 98% | Lake Grosse Fuchskuhleclone FukuS59 | AJ290042 | |||||||||
| 24 | 4 | Sphingobacteriaceae | 100% | 96% | Tatachia forest soil cloneTSC56 | EU359966 | |||||||||||||||
| Verucomicrobia | 25 | 4 | 2 | Subdivision5 | 78% | 97% | Lake Kinneret sedimentclone d0-26 | AM409824 | |||||||||||||
| Acidobacteria | 26 | 4 | 2 | 8 | 6 | 4 | 2 | Holophagaceae | 100% | 96% | Geotrix fermentansATCC 700665 | U41563 | |||||||||
| Chloroplasts | 27 | 13 | 2 | 7 | 55 | 2 | 13 | Bacillariophyta | 87% | 97% | Parker river clonePRD18F11 | AY948053 | |||||||||
| 28 | 4 | 2 | 8 | Chlorarachniophyceae | 40% | 93% | Parker river clonePRD18D01 | AY948021 | |||||||||||||
| 29 | 2 | 20 | 4 | 15 | 12 | 2 | 6 | Chlorarachniophyceae | 68% | 93% | Adriondack lake cloneADK-HDe02-54 | EF520517 | |||||||||
| 30 | 9 | 8 | 17 | 29 | Cryptomonadaceae | 100% | 94% | Adirondack lake cloneADK-SGh02-76 | EF520521 | ||||||||||||
| 31 | 4 | 8 | 13 | 2 | 17 | Cryptomonadaceae | 100% | 98% | Parker river clonePRD18E12 | AY948043 | |||||||||||
| 32 | 8 | Chlorophyta | 100% | 91% | Polytoma oviformecloroplast | AF374188 | |||||||||||||||
| Rare OTUs (%)* | 6 | 2 | 2 | 7 | 7 | 2 | 8 | 4 | 4 | 4 | 2 | ||||||||||
| Single OTUs (%)# | 11 | 6 | 13 | 7 | 13 | 6 | 23 | 23 | 17 | 4 | 27 | 23 | 13 | 10 | |||||||
| Total No. ofclones | 54 | 47 | 45 | 45 | 46 | 53 | 52 | 53 | 48 | 50 | 49 | 47 | 53 | 48 | |||||||
| Coverage (%) | 83 | 91 | 84 | 87 | 80 | 92 | 69 | 77 | 79 | 92 | 69 | 74 | 87 | 90 | |||||||
*Rare OTUs: OTUs that occur only once in one clone library;
#
Single OTUs: OTUs that occur only once in at least two clone libraries.