Cellulose degradation by micromonosporas recovered from freshwater lakes and classification of these actinomycetes by DNA gyrase B gene sequencing.

A number of Micromonospora strains isolated from the water column, sediment, and cellulose baits placed in freshwater lakes were shown to be able to degrade cellulose in lake water without any addition of nutrients. A selective isolation method was also developed to demonstrate that CFU arose from both spores and hyphae that inhabit the lake environment. Gyrase B gene sequencing performed on the isolates identified a number of new centers of variation within Micromonospora, but the most actively cellulolytic strains were recovered in a single cluster that equated with the type species of the genus, M. chalcea.

Detection of novel Fibrobacter populations in landfill sites and determination of their relative abundance via quantitative PCR.

Members of the bacterial genus Fibrobacter have long been considered important components of the anaerobic cellulolytic community in the herbivore gut, but their presence and activity in other environments is largely unknown. In this study, a specific polymerase chain reaction (PCR) primer set, targeting the 16S rRNA gene of Fibrobacter spp., was applied to community DNA from five landfill sites followed by temporal thermal gel electrophoresis (TTGE) analysis of cloned amplification products. Phylogenetic analysis of clone sequences indicated the presence of novel clusters closely related to the genus Fibrobacter. There are two named species, Fibrobacter succinogenes and F. intestinalis, and only two of the 58 sequenced clones were identified with them, and both were F. succinogenes. The clone sequences from landfill were recovered in five distinct clusters within the Fibrobacter lineage, and four of these were novel. Quantitative PCR (qPCR) assays of reverse-transcribed community RNA from landfill leachates and rumen fluid samples indicated that the abundance of Fibrobacter spp. relative to total bacteria varied from 0.2% to 40% in landfill, and 21% to 32% in the rumen, and these data demonstrate that fibrobacters can be a significant component of the microbial community in landfill ecosystems. This is the first evidence for Fibrobacter spp. outside the gut ecosystem, and as the only cultivated representatives of this group are actively cellulolytic, their diversity and abundance points to a possible role in cellulose hydrolysis in landfill, and perhaps other anaerobic environments also.

Molecular biological detection of anaerobic gut fungi (Neocallimastigales) from landfill sites.

Oligonucleotide primers were designed for the 18S rRNA genes of members of the Neocallimastigales and used in a nested PCR protocol to amplify 787-bp fragments of DNA from landfill site samples. The specificities of the primers were confirmed by phylogenetic analysis of the environmental clone sequences, and this method can therefore now be used to investigate the ecology of the obligately anaerobic fungi. To our knowledge, this is the first demonstration of the occurrence of members of the Neocallimastigales outside the mammalian gut, and their distribution across the landfill samples examined here suggests that they are actively involved in cellulose degradation.