Methanol-induced shifts inacidobacterial diversity and isolation of a novel acidobacteriumfrom soil

Eichorst, S.A., B.S. Stevenson, C.D. Engles, J.A. Breznak, and T.M. Schmidt

Presented at the ASM in Seattle (2003-09-18 to 2017-12-05 )

Soil is a heterogeneous environment containing over 4,000 species of bacteria per gram. However, the physiological diversity of the soil microbiota is poorly understood, since most of its phylogenetic diversity is not well represented in culture, such as the Acidobacteria division. We sought to extend observations done by others suggesting that some acidobacteria are methylotrophs, based on the accumulation of 13C in acidobacterial DNA upon incubation of soils with 13C -methanol. Microcosms were established with soil from the Kellogg Biological Station Long Term Ecological Research (KBS LTER) site in Hickory Corners, Michigan and incubated with methanol. A steady decrease in methanol was observed over 40 days of incubation. Statistical analyses (LIBSHUFF), performed on PCR-amplified Acidobacterium 16S rDNA libraries made from soil samples before and after treatment, suggested that methanol enriched for a phylogenetically cohesive group of acidobacteria. The clade enriched with methanol also accommodated a novel Acidobacterium (strain KBS 89) we recently isolated from the same soil; using minimal media incubated under 95% air/ 5% CO2. Homologous media incubated in air alone did not yield any acidobacteria detectable by “Plate Wash PCR” (a facile screening technique developed in our laboratory), suggesting that elevated levels of CO2 facilitated the growth of the isolate. Acidobacterium str. KBS 89 is a nonmotile rod measuring 0.5 μm x 1μm; catalase and oxidase negative; and produces an extracellular matrix causing cells to stick together tightly in colonies and form clumps in liquid culture. The closest phylogenetic relative to strain KBS 89 is an Acidobacterium recently isolated from an Australian pasture. Based on 16S rRNA, we estimate that Acidobacterium in KBS LTER soil represent 1-7% of the total microbial population. Acidobacterium str. KBS 89 and the ecological role of acidobacteria in soil is the object of continued investigation in our laboratory.

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