Culturability of Novel Acidobacteria in German Grass- and Woodland Soils

Culturability of novel Acidobacteria in German grass- and woodland soils

V. Baumgartner, P.K. Wüst, B.U. Fösel, and J. Overmann

Leibniz Institute DSMZ - German Collection of Microorganisms and Cell Cultures,Braunschweig,Department of Microbial Ecology and Diversity Research, Germany

Acidobacteriaon average account for 20% of all soil bacteria and are physiologically active in situ. Culture-independent studies indicate that Acidobacteria are nearly as diverse as the Proteobacteria and currently comprise 26 distinct phylogenetic subdivisions (sd). However, until now only a few strains from sd 1, 3, and 8, have been validly described. Genome analysis revealed the ability of Acidobacteriato use complex substrates as carbon sources.Within the German Biodiversity Exploratories project we focus on functionalinterrelations betweenAcidobacteria and land use. Six extensively managed sitesfrom the ExploratoriesSchwäbische Alb, HainichDün, and SchorfheideChorin,one grassland and one woodland soil per exploratory,were selected for a high throughput cultivation approach.Microtiter plates were inoculated with 10 and 50 cells per well, respectively, using five media at in situpH.The media tested contained (i) highly diluted carbon sources (HD1:10), (ii) low amounts of sugars, fatty acids, and amino acids(CMix), (iii) soluble humic acids (e.g., sodium salicylate, furfural, phthalic acid), (iv) insoluble humic acids (e.g.,quercetin, coumestrol, solanine), and (v) a mix of polymeric substrates (e.g., chitin, pectin, cellulose). Culturability of total aerobes ranged from below 0.2% (SchorfheideChorin, grassland, soluble humic acids) to 9.2% (Schwäbische Alb, woodland, HD1:10).Acidobacteria-positve wells were identified viaa specific PCR approach. The percentages of cultured Acidobacteriaamong all cultured Bacteriaranged from 0% (SchorfheideChorin, woodland, polymeric substrates) to 19.5% (Schwäbische Alb, woodland, polymeric substrates).The Acidobacteriarecovered were affiliated with sd1, 3, 4, and 6. Inpolymers-supplemented media, only representatives of sd1were detected.In contrast, most members of sd6 Acidobacteria were cultivated in C-mix medium.For both, total aerobes and Acidobacteria, cultivation success was highest with media containing easily available carbon sources, indicating that low amounts of these substrates favor growth of soil bacteria, in particular Acidobacteria. Characterization of novelAcidobacteria as relevant members of the soil microbial community will improve our knowledge about biogeochemical cycling in soils.