Key points are not available for this paper at this time.
Active members of the bacterial community in the sediment of Lake Washington, with special emphasis on C1 utilizers, were identified by employing two complementary culture-independent approaches: reverse transcription of environmental mRNA and 16S rRNA combined with PCR (RT-PCR) and stable-isotope probing (SIP) of DNA with the 13C-labeled C1 substrates methanol, methylamine, formaldehyde, and formate. Analysis of RT-PCR-amplified fragments of 16S rRNA-encoding genes revealed that gammaproteobacterial methanotrophs belonging to Methylobacter and Methylomonas dominate the active methylotroph population, while only one other known methylotrophic lineage, Methylophilaceae, was detected via this approach. Analysis of RT-PCR-amplified functional genes, pmoA and fae, allowed detection of alphaproteobacterial (Methylosinus) and gammaproteobacterial (Methylobacter, Methylomonas, and Methylomicrobium) methanotrophs, methylotrophs of the genus Methylobacterium, and yet-unidentified proteobacteria. SIP experiments allowed detection of a broad variety of groups actively metabolizing C1 compounds. Comparisons between 16S rRNA gene pools amplified from 13CDNA and from 12CDNA revealed that the proportion of Methylophilus-related sequences increased in the presence of 13Cmethanol, 13Cmethylamine, and 13Cformaldehyde; Novosphingobium-related sequences were enriched in the presence of 13Cmethanol; Gemmatimonadaceae-related sequences were enriched in the presence of 13Cformaldehyde and 13Cformate; and Xanthomonadaceae-related sequences were enriched in the presence of 13Cformate. Analysis of fae genes amplified from 13CDNAs isolated from different microcosms revealed specific shifts in populations in response to a specific C1 compound: Methylosinus sequences dominated the 13Cmethanol microcosm pool, and beta- and gammaproteobacterial sequences dominated the 13Cmethylamine microcosm pool. The 13Cformaldehyde microcosm was dominated by betaproteobacterial sequences and by sequences of a nonaffiliated group, while the 13Cformate microcosm was dominated by alpha- and betaproteobacterial sequences. Overall, these data point toward the presence of a diverse population of active methylotrophs in Lake Washington sediments and toward the existence of yet-uncultivated organisms.
Nercessian et al. (Tue,) studied this question.