TABLE 1.
16S rRNA gene phylotype distribution in libraries obtained from total RNA isolated from Lake Washington sediment and from [13C]DNA and [12C]DNA fractions obtained from the microcosm experimentsa
| Phylogenetic group | Phylotype(s) | No. of clones in library
|
||||||||
|---|---|---|---|---|---|---|---|---|---|---|
| RNA | Methanol
|
Methylamine
|
Formaldehyde
|
Formate
|
||||||
| [13C] DNA | [12C] DNA | [13C] DNA | [12C] DNA | [13C] DNA | [12C] DNA | [13C] DNA | [12C] DNA | |||
| Proteobacteria | ||||||||||
| Betaproteobacteria | ||||||||||
| Comamonadaceae | pLW-1, pLW-2, pLW-3, pLW-4 | 17 | 3 | 3 | 1 | |||||
| Oxalobacteraceae | pLW-5, pLW-6 | 2 | 1 | 2 | ||||||
| Nitrosomonadaceae | pLW-7, pLW-8, pLW-9, pLW-10 | 9 | ||||||||
| Methylophylaceae | pLW-11, pLW-12, pLW-13 | 1 | 22 | 10 | 43 | 3 | 18 | 9 | ||
| Unclassified Betaproteobacteria | pLW-16 | 1 | ||||||||
| Gammaproteobacteria | ||||||||||
| Methylobacter/Methylomonas | pLW-17, pLW-18, pLW-19, pLW-20, pLW-21, pLW-22 | 16 | ||||||||
| Pseudomonas | pLW-23, pLW-24 | 3 | 4 | 1 | 1 | |||||
| Achromatium | pLW-25 | 2 | ||||||||
| Xanthomonadaceae | pLW-26, pLW-27 | 1 | 5 | |||||||
| Thioploca/Beggiatoa | pLW-28, pLW-29 | 5 | ||||||||
| Unclassified Gammaproteobacteria | pLW-30, pLW-31, pLW-32 | 2 | 1 | 4 | ||||||
| Alphaproteobacteria | ||||||||||
| Caulobacterales | pLW-33 | 1 | ||||||||
| Rhodobacterales | pLW-34 | 1 | ||||||||
| Sphingomonadales | pLW-35, pLW-36, pLW-37 | 17 | 2 | |||||||
| Unclassified Alphaproteobacteria | pLW-38, pLW-39, pLW-40 | 1 | 2 | |||||||
| Deltaproteobacteria | ||||||||||
| Syntrophus | pLW-41 | 1 | ||||||||
| Polyangiaceae | pLW-42 | 1 | ||||||||
| Myxococcaceae | pLW-43 | 3 | ||||||||
| Geobacteraceae | pLW-44 | 1 | ||||||||
| Unclassified Deltaproteobacteria | pLW-45, pLW-46, pLW-47 | 3 | 3 | 1 | ||||||
| Bacteroidetes | ||||||||||
| Flexibacteraceae | pLW-48 | 2 | ||||||||
| Saprospiraceae | pLW-49 | 2 | ||||||||
| Sphingobacteriaceae | pLW-50, pLW-51 | 3 | ||||||||
| Unclassified Bacteroidetes | pLW-52, pLW-53, pLW-54, pLW-55, pLW-56, pLW-57 | 15 | 3 | 1 | 1 | |||||
| Acidobacteria | ||||||||||
| Holophaga/Geothrix | pLW-58, pLW-59, pLW-60, pLW-61, pLW-62, pLW-63 | 6 | 1 | 1 | 31 | 33 | 1 | |||
| Unclassified Acidobacteria | pLW-64, pLW-65 | 2 | 1 | |||||||
| Nitrospirae (unclassified) | pLW-66, pLW-67, pLW-68 | 2 | 1 | 4 | 1 | 2 | ||||
| WS3 | pLW-69, pLW-70 | 3 | 3 | |||||||
| Actinobacteria | ||||||||||
| Acidimicrobiaceae | pLW-71, pLW-72 | 3 | 1 | 1 | ||||||
| Rubrobacteraceae | pLW-73, pLW-74, pLW-75 | 2 | 2 | |||||||
| Unclassified Actinobacteria | pLW-76, pLW-77 | 1 | 1 | 1 | ||||||
| Gemmatimonadetes (Gemmatimonadaceae) | pLW-78, pLW-79, pLW-80, pLW-81, pLW-82, pLW-83, pLW-84, pLW-85, pLW-86, pLW-87 | 3 | 2 | 4 | 1 | 8 | 4 | |||
| Verrumicrobium (unclassified) | pLW-88, pLW-89 | 5 | ||||||||
| Planctomycetes (unclassified) | pLW-90, pLW-91 | 1 | 2 | |||||||
| Chlorobi (unclassified) | pLW-92, pLW-93 | 1 | 4 | |||||||
| Spirochaetes (Leptospiraceae) | pLW-94 | 1 | ||||||||
| Chloroflexi (unclassified) | pLW-95, pLW-96, pLW-97 | 1 | 1 | 3 | 3 | |||||
| Fibrobacteres (unclassified) | pLW-98 | 1 | ||||||||
| Unclassified Bacteria | pLW-99 | 3 | ||||||||
| pLW-100 | 3 | 1 | ||||||||
| pLW-101 | 2 | |||||||||
| pLW-102 | 2 | |||||||||
| pLW-103 | 1 | |||||||||
| pLW-104 | 2 | |||||||||
| pLW-105 | 1 | |||||||||
| pLW-106 | 1 | |||||||||
| Total | 107 | 42 | 26 | 43 | 14 | 67 | 66 | 26 | 28 | |
a
Classification is according to the Ribosomal Database Project-II (http://rdp.cme.msu.edu/classifier.jsp). Phylotypes were defined as sequences less than 97% similar (41). Unclassified phylotypes could not be assigned with a bootstrap confidence estimate above the default threshold value of the RDP Classifier (80%).